Sun Nov 24 15:05:37 UTC 2024 I: starting to build vg/unstable/amd64 on jenkins on '2024-11-24 15:05' Sun Nov 24 15:05:37 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_4/38045/console.log Sun Nov 24 15:05:37 UTC 2024 I: Downloading source for unstable/vg=1.59.0+ds-0.1 --2024-11-24 15:05:38-- http://deb.debian.org/debian/pool/main/v/vg/vg_1.59.0%2bds-0.1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2839 (2.8K) [text/prs.lines.tag] Saving to: ‘vg_1.59.0+ds-0.1.dsc’ 0K .. 100% 382M=0s 2024-11-24 15:05:38 (382 MB/s) - ‘vg_1.59.0+ds-0.1.dsc’ saved [2839/2839] Sun Nov 24 15:05:38 UTC 2024 I: vg_1.59.0+ds-0.1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: vg Binary: vg, vg-docs Architecture: amd64 arm64 ppc64el mips64el s390x riscv64 x32 all Version: 1.59.0+ds-0.1 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe Homepage: https://github.com/vgteam/vg#vg Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/vg Vcs-Git: https://salsa.debian.org/med-team/vg.git Testsuite: autopkgtest Testsuite-Triggers: libvcflib-tools Build-Depends: debhelper-compat (= 13), pv , bsdextrautils | bsdmainutils, zlib1g-dev, rs, libffi-dev, bwa , protobuf-compiler, libprotoc-dev, libprotobuf-dev, libjansson-dev, libbz2-dev, libtinfo6, libncurses-dev, automake, libtool, jq, samtools , unzip, librdf0-dev, cmake, pkgconf, bc, gtk-doc-tools, raptor2-utils , rasqal-utils , bison, flex, gawk, liblz4-dev, liblzma-dev, libcairo2-dev, libpixman-1-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 , libdivsufsort-dev, libtsl-hopscotch-map-dev, libvcflib-dev (>= 1.0.1), libvcflib-tools , libhts-dev, help2man , python3:any, libsimde-dev, libzstd-dev Build-Depends-Indep: doxygen , graphviz Package-List: vg deb science optional arch=amd64,arm64,ppc64el,mips64el,s390x,riscv64,x32 vg-docs deb doc optional arch=all Checksums-Sha1: 9cceebb48fb18c8618654723085c6aaa4321f386 69705744 vg_1.59.0+ds.orig.tar.xz ddd7d9f6b17fee1f35ac6d3a00de3d7b2e6e491c 117112 vg_1.59.0+ds-0.1.debian.tar.xz Checksums-Sha256: 17e43b91bce35905caf9af98e3b839eeff296af7105c1df818eb81004e6ab144 69705744 vg_1.59.0+ds.orig.tar.xz dfd2b9a5f833d45b9b5632b651de59668380352bc87fa2654b2c2c7acf6c423b 117112 vg_1.59.0+ds-0.1.debian.tar.xz Files: e8aff1b3feff38a4085bf4fbee107ac9 69705744 vg_1.59.0+ds.orig.tar.xz 66279467d1d25d09cdba16f34999a366 117112 vg_1.59.0+ds-0.1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQHEBAEBCgAuFiEEQGIgyLhVKAI3jM5BH1x6i0VWQxQFAmc/WKIQHGJhZ2VAZGVi aWFuLm9yZwAKCRAfXHqLRVZDFHNzDAChrlW8GHppGU1D++m3+LBMHm1tEC4x4pa4 85La0aNeKtBpMqH6R7GpLZJ2HkdjXCqWdKXv60UYX7ughXFl30EQoAT8OM6+gN1w XUfB4XXa/OAvF0grSmIE08PL4nnvGcJlnXd5vW+DF/R8Ll7bIJLtWIn2kHV28uTk 9Faz9DRF4xEtNkVhHBcmlwxott+Zhf2Prt6XyjhUHegCRAd3aAcVrZQl87cR+gIj JpVjf1H9jBG4HhgZ7yxjDQmaosSgAuKf41GAyAl8YbxeLTcIfg3KYQ+LOWMDiRWv bucCUzqPlanDR5OtNk1+ORER59FE83oXSq1tLUMAeP53sE9jhVLFafwjWc5YqsRz XHkA0FGcYdlbcYUkRaXBKPHyvcBXrE81cA4CO9Afa8C3kgDwArYfq5OY08CE++/u 3t9vc+kT+wE9w3x6W81ywxyPchFlTEhjnoAZJ2kUhlVgsGNTT+9wi5Cbq9HFW6Lt 17nlcUFy3vPmaFg8qzO9Kte7eCqp1Q0= =YEjD -----END PGP SIGNATURE----- Sun Nov 24 15:05:38 UTC 2024 I: Checking whether the package is not for us Sun Nov 24 15:05:38 UTC 2024 I: Starting 1st build on remote node ionos15-amd64.debian.net. Sun Nov 24 15:05:38 UTC 2024 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Sun Nov 24 16:08:58 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Dec 27 09:28:42 -12 2025 I: pbuilder-time-stamp: 1766870922 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [vg_1.59.0+ds-0.1.dsc] I: copying [./vg_1.59.0+ds.orig.tar.xz] I: copying [./vg_1.59.0+ds-0.1.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Nov 21 15:58:26 2024 gpgv: using RSA key 406220C8B8552802378CCE411F5C7A8B45564314 gpgv: issuer "bage@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./vg_1.59.0+ds-0.1.dsc: no acceptable signature found dpkg-source: info: extracting vg in vg-1.59.0+ds dpkg-source: info: unpacking vg_1.59.0+ds.orig.tar.xz dpkg-source: info: unpacking vg_1.59.0+ds-0.1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying avoid_abs_confusion dpkg-source: info: applying gcc-12 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_fermi-lite 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 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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2027625/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='b2f48b63428f4ce5a46bd0722a51613e' 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='2027625' 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.4o9ZkNWR/pbuilderrc_xl91 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.4o9ZkNWR/b1 --logfile b1/build.log vg_1.59.0+ds-0.1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2027625/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), pv, bsdextrautils | bsdmainutils, zlib1g-dev, rs, libffi-dev, bwa, protobuf-compiler, libprotoc-dev, libprotobuf-dev, libjansson-dev, libbz2-dev, libtinfo6, libncurses-dev, automake, libtool, jq, samtools, unzip, librdf0-dev, cmake, pkgconf, bc, gtk-doc-tools, raptor2-utils, rasqal-utils, bison, flex, gawk, liblz4-dev, liblzma-dev, libcairo2-dev, libpixman-1-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, libdivsufsort-dev, libtsl-hopscotch-map-dev, libvcflib-dev (>= 1.0.1), libvcflib-tools, libhts-dev, help2man, python3:any, libsimde-dev, libzstd-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 ... 19966 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 bsdextrautils | bsdmainutils; however: Package bsdextrautils is not installed. 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 libncurses-dev; however: Package libncurses-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 pkgconf; however: Package pkgconf 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 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 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 libzstd-dev; however: Package libzstd-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} bwa{a} ca-certificates{a} cmake{a} cmake-data{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docbook{a} docbook-to-man{a} docbook-xml{a} docbook-xsl{a} doxygen{a} dwz{a} elfutils{a} fastahack{a} file{a} flex{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gawk{a} gettext{a} gettext-base{a} girepository-tools{a} graphviz{a} groff-base{a} gtk-doc-tools{a} help2man{a} icu-devtools{a} intltool-debian{a} jq{a} krb5-multidev{a} libabsl20230802{a} libann0{a} libaom3{a} libarchive-zip-perl{a} libarchive13t64{a} libasm1t64{a} libavif16{a} libbackward-cpp-dev{a} libblas3{a} libblkid-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcairo-gobject2{a} libcairo-script-interpreter2{a} libcairo2{a} libcairo2-dev{a} libcdt5{a} libcgraph6{a} libclang-cpp19{a} libclang1-19{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdatrie1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdebuginfod-common{a} libdebuginfod1t64{a} libdeflate-dev{a} libdeflate0{a} libdisorder-dev{a} libdisorder0{a} libdivsufsort-dev{a} libdivsufsort3{a} libdw-dev{a} libdw1t64{a} libedit2{a} libelf-dev{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libfastahack-dev{a} libfastahack0{a} libffi-dev{a} libfile-stripnondeterminism-perl{a} libfml-dev{a} libfml0{a} libfmt10{a} libfontconfig-dev{a} libfontconfig1{a} libfreetype-dev{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libgfortran5{a} libgio-2.0-dev{a} libgio-2.0-dev-bin{a} libgirepository-2.0-0{a} libglib2.0-0t64{a} libglib2.0-bin{a} libglib2.0-data{a} libglib2.0-dev{a} libglib2.0-dev-bin{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libgts-0.7-5t64{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libice-dev{a} libice6{a} libicu-dev{a} libicu72{a} libidn2-dev{a} libimagequant0{a} libjansson-dev{a} libjbig0{a} libjemalloc-dev{a} libjemalloc2{a} libjpeg62-turbo{a} libjq1{a} libjson-c5{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblab-gamut1{a} liblapack3{a} libldap-2.5-0{a} libldap-dev{a} liblerc4{a} libllvm19{a} liblocale-gettext-perl{a} libltdl7{a} liblz4-dev{a} liblzma-dev{a} liblzo2-2{a} libmagic-mgc{a} libmagic1t64{a} libmhash2{a} libmount-dev{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libnsl2{a} libonig5{a} libosp5{a} libp11-kit-dev{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpathplan4{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libpixman-1-0{a} libpixman-1-dev{a} libpkgconf3{a} libpng-dev{a} libpng16-16t64{a} libproc2-0{a} libprotobuf-dev{a} libprotobuf-lite32t64{a} libprotobuf32t64{a} libprotoc-dev{a} libprotoc32t64{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libraptor2-0{a} libraptor2-dev{a} libraqm0{a} librasqal3-dev{a} librasqal3t64{a} librav1e0.7{a} librdf0-dev{a} librdf0t64{a} libreadline8t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libselinux1-dev{a} libsepol-dev{a} libsharpyuv0{a} libsigsegv2{a} libsimde-dev{a} libsm-dev{a} libsm6{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libsparsehash-dev{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libssw-dev{a} libssw0{a} libsvtav1enc2{a} libsysprof-capture-4-dev{a} libtabixpp-dev{a} libtabixpp0t64{a} libtasn1-6-dev{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtsl-hopscotch-map-dev{a} libuchardet0{a} libunbound8{a} libuv1t64{a} libvcflib-dev{a} libvcflib-tools{a} libvcflib2{a} libwebp7{a} libwfa2-0{a} libwfa2-dev{a} libx11-6{a} libx11-data{a} libx11-dev{a} libxau-dev{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-render0-dev{a} libxcb-shm0{a} libxcb-shm0-dev{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxft2{a} libxml2{a} libxml2-dev{a} libxmu6{a} libxpm4{a} libxrender-dev{a} libxrender1{a} libxslt1-dev{a} libxslt1.1{a} libxss1{a} libxt6t64{a} libyajl-dev{a} libyajl2{a} libyuv0{a} libz3-4{a} libzstd-dev{a} littler{a} m4{a} man-db{a} media-types{a} native-architecture{a} netbase{a} nettle-dev{a} opensp{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} protobuf-compiler{a} pv{a} python3{a} python3-autocommand{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-lxml{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{a} python3-pygments{a} python3-typeguard{a} python3-typing-extensions{a} python3.12{a} python3.12-minimal{a} r-base-core{a} r-cran-cli{a} r-cran-colorspace{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-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-pkgconfig{a} r-cran-pkgkitten{a} r-cran-plyr{a} r-cran-r6{a} r-cran-rcolorbrewer{a} r-cran-rcpp{a} r-cran-rlang{a} r-cran-scales{a} r-cran-tibble{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-viridislite{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-core-dev{a} x11proto-dev{a} xdg-utils{a} xml-core{a} xorg-sgml-doctools{a} xsltproc{a} xtrans-dev{a} xxd{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl fonts-liberation krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libfl-dev libgpm2 libgts-bin libheif-plugin-aomenc libheif-plugin-x265 libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libpng-tools libsasl2-modules libtasn1-doc libx11-protocol-perl linux-sysctl-defaults lynx psmisc publicsuffix python3-bs4 python3-cssselect python3-html5lib r-base-dev r-cran-abind r-cran-bit64 r-cran-callr r-cran-covr r-cran-crayon r-cran-data.table r-cran-dbi r-cran-dichromat r-cran-digest r-cran-doparallel r-cran-dplyr r-cran-foreach r-cran-formattable r-cran-fs r-cran-generics r-cran-hexbin r-cran-hmisc r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-iterators r-cran-itertools r-cran-jpeg r-cran-kernlab r-cran-kernsmooth r-cran-knitr r-cran-lintr r-cran-lubridate r-cran-mapproj r-cran-maps r-cran-mockery r-cran-mockr r-cran-multcomp r-cran-mvtnorm r-cran-pkgdown r-cran-png r-cran-processx r-cran-profvis r-cran-ps r-cran-quantreg r-cran-ragg r-cran-rmarkdown r-cran-rpart r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-sf r-cran-shiny r-cran-shinyjs r-cran-stringi r-cran-svglite r-cran-testthat r-cran-tidyverse r-cran-unitizer r-cran-usethis r-cran-vcd r-cran-vdiffr r-cran-viridis r-cran-waldo r-cran-whoami r-cran-xml2 r-cran-zeallot r-doc-html r-recommended redland-utils shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 382 newly installed, 0 to remove and 0 not upgraded. Need to get 265 MB of archives. After unpacking 1090 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 flex amd64 2.6.4-8.2+b3 [423 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libsigsegv2 amd64 2.14-1+b2 [34.4 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 gawk amd64 1:5.2.1-2+b1 [674 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libdebuginfod-common all 0.192-4 [23.7 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-3 [255 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Get: 30 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 bc amd64 1.07.1-4 [103 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 bison amd64 2:3.8.2+dfsg-1+b2 [1170 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 bwa amd64 0.7.18-1 [212 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.31.1-1 [2267 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.31.1-1 [11.9 MB] Get: 69 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.1-1+b1 [54.8 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 76 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 docbook all 4.5-11 [126 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libosp5 amd64 1.5.2-15 [964 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 opensp amd64 1.5.2-15 [450 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 docbook-to-man amd64 1:2.0.0-47 [73.6 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 docbook-xml all 4.5-13 [77.4 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 docbook-xsl all 1.79.2+dfsg-7 [1221 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.3-2 [26.0 MB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libclang-cpp19 amd64 1:19.1.3-2 [13.2 MB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libclang1-19 amd64 1:19.1.3-2 [7622 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libfmt10 amd64 10.1.1+ds1-4 [127 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 doxygen amd64 1.9.8+ds-2+b3 [5011 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libdw1t64 amd64 0.192-4 [255 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libasm1t64 amd64 0.192-4 [28.4 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.4.0-1+b1 [63.6 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.11.0-1 [359 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libjson-c5 amd64 0.18+ds-1 [46.0 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libdebuginfod1t64 amd64 0.192-4 [32.4 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 elfutils amd64 0.192-4 [505 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-4+b2 [4908 B] Get: 107 http://deb.debian.org/debian unstable/main amd64 libfastahack0 amd64 1.0.0+dfsg-11+b2 [26.4 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 fastahack amd64 1.0.0+dfsg-11+b2 [12.7 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 native-architecture all 0.2.3 [2108 B] Get: 117 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.82.2-3 [1501 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libgirepository-2.0-0 amd64 2.82.2-3 [139 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 girepository-tools amd64 2.82.2-3 [145 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libann0 amd64 1.1.2+doc-9+b1 [25.1 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libcdt5 amd64 2.42.4-2+b1 [40.5 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libcgraph6 amd64 2.42.4-2+b1 [64.2 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.11.0-1 [1879 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.0-1+b1 [550 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libgav1-1 amd64 0.19.0-2+b2 [350 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 librav1e0.7 amd64 0.7.1-7+b2 [936 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc2 amd64 2.2.1+dfsg-2 [2173 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1897.20241115-1 [172 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.1.1-1 [117 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-dav1d amd64 1.19.3-1 [11.2 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libde265-0 amd64 1.0.15-1+b2 [189 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-libde265 amd64 1.19.3-1 [15.0 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libheif1 amd64 1.19.3-1 [489 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.1-1+b2 [14.1 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b2 [56.3 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libgd3 amd64 2.3.3-12+b1 [126 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libgts-0.7-5t64 amd64 0.7.6+darcs121130-5.2+b1 [160 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.4.7-8 [393 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [223 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [54.2 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [35.2 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libpathplan4 amd64 2.42.4-2+b1 [42.8 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libgvc6 amd64 2.42.4-2+b1 [685 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libgvpr2 amd64 2.42.4-2+b1 [193 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 liblab-gamut1 amd64 2.42.4-2+b1 [198 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-3+b3 [58.8 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 libxaw7 amd64 2:1.0.16-1 [212 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 graphviz amd64 2.42.4-2+b1 [616 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 5.3.0-1+b1 [1676 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 190 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 xsltproc amd64 1.1.35-1.1+b1 [115 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 gtk-doc-tools all 1.34.0-1 [328 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-5+b1 [210 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 libonig5 amd64 6.9.9-1+b1 [189 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libjq1 amd64 1.7.1-3+b1 [164 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 jq amd64 1.7.1-3+b1 [77.8 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-3 [59.5 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-3 [41.7 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-3 [42.0 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-3 [53.5 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-3 [126 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libbackward-cpp-dev all 1.6-1 [34.3 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 uuid-dev amd64 2.40.2-11 [47.2 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libblkid-dev amd64 2.40.2-11 [204 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-3.2+b1 [10.6 MB] Get: 210 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83.0 amd64 1.83.0-3.2+b1 [347 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83-dev amd64 1.83.0-3.2+b1 [376 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Get: 213 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 liblzo2-2 amd64 2.10-3+b1 [55.1 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 libcairo-script-interpreter2 amd64 1.18.2-2 [58.8 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 libpng-dev amd64 1.6.44-2 [366 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 libfreetype-dev amd64 2.13.3+dfsg-1 [622 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 libfontconfig-dev amd64 2.15.0-1.1+b1 [414 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 libffi-dev amd64 3.4.6-1 [60.6 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 libsepol-dev amd64 3.7-1 [370 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.44-4 [261 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 libpcre2-32-0 amd64 10.44-4 [248 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 libpcre2-posix3 amd64 10.44-4 [60.3 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 libpcre2-dev amd64 10.44-4 [790 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 libselinux1-dev amd64 3.7-3+b1 [160 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 libmount-dev amd64 2.40.2-11 [29.0 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 libsysprof-capture-4-dev amd64 47.1-1 [47.6 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 libgio-2.0-dev amd64 2.82.2-3 [1675 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 libglib2.0-data all 2.82.2-3 [1275 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 libglib2.0-bin amd64 2.82.2-3 [127 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 libgio-2.0-dev-bin amd64 2.82.2-3 [163 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 libglib2.0-dev-bin amd64 2.82.2-3 [51.5 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 libglib2.0-dev amd64 2.82.2-3 [52.3 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 libpixman-1-dev amd64 0.44.0-3 [11.4 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 x11proto-dev all 2024.1-1 [603 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 x11proto-core-dev all 2024.1-1 [3312 B] Get: 243 http://deb.debian.org/debian unstable/main amd64 libice-dev amd64 2:1.1.1-1 [73.8 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 libsm-dev amd64 2:1.2.4-1 [37.7 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 libxau-dev amd64 1:1.0.11-1 [23.6 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 libxdmcp-dev amd64 1:1.1.5-1 [44.3 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 libxcb1-dev amd64 1.17.0-2+b1 [181 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 libx11-dev amd64 2:1.8.10-2 [891 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 libxcb-render0-dev amd64 1.17.0-2+b1 [118 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0-dev amd64 1.17.0-2+b1 [108 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 libxext-dev amd64 2:1.3.4-1+b2 [104 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 libxrender-dev amd64 1:0.9.10-1.1+b2 [35.8 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 libcairo2-dev amd64 1.18.2-2 [43.0 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1 [598 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.8-2 [449 kB] Get: 258 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.8-2 [449 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-2+b1 [208 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.19.0-3+b3 [98.9 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2+b2 [329 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2+b2 [642 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10-1+b1 [1317 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.8-2 [1391 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-3 [15.7 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.5.18+dfsg-3+b1 [303 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.4.0-1+b1 [87.2 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.6.0-1 [23.8 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.6.0-1 [170 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.3.2-2 [2742 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 276 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-1+b1 [365 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.11.0-1 [472 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.22-1 [55.8 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 libdisorder-dev amd64 0.0.2+git20130809.8062ee1-4+b2 [4912 B] Get: 280 http://deb.debian.org/debian unstable/main amd64 libdivsufsort3 amd64 2.0.1-6+b1 [45.9 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 libdivsufsort-dev amd64 2.0.1-6+b1 [19.1 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 libelf-dev amd64 0.192-4 [93.2 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 libdw-dev amd64 0.192-4 [335 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 libfastahack-dev amd64 1.0.0+dfsg-11+b2 [27.9 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 libfml0 amd64 0.1+git20190320.b499514-1+b2 [70.3 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 libfml-dev amd64 0.1+git20190320.b499514-1+b2 [82.0 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.20+ds-2 [1701 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-5+b1 [10.4 MB] Get: 293 http://deb.debian.org/debian unstable/main amd64 libjansson-dev amd64 2.14-2+b3 [43.2 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 libjemalloc2 amd64 5.3.0-2+b2 [275 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 libjemalloc-dev amd64 5.3.0-2+b2 [491 kB] Get: 296 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get: 297 http://deb.debian.org/debian unstable/main amd64 liblz4-dev amd64 1.9.4-3+b1 [83.2 kB] Get: 298 http://deb.debian.org/debian unstable/main amd64 libmhash2 amd64 0.9.9.9-10 [92.4 kB] Get: 299 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get: 300 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5-2+b1 [351 kB] Get: 301 http://deb.debian.org/debian unstable/main amd64 libpaper1 amd64 1.1.29+b2 [12.8 kB] Get: 302 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 1.1.29+b2 [9236 B] Get: 303 http://deb.debian.org/debian unstable/main amd64 libprotobuf32t64 amd64 3.21.12-10+b1 [982 kB] Get: 304 http://deb.debian.org/debian unstable/main amd64 libprotobuf-lite32t64 amd64 3.21.12-10+b1 [274 kB] Get: 305 http://deb.debian.org/debian unstable/main amd64 libprotobuf-dev amd64 3.21.12-10+b1 [1329 kB] Get: 306 http://deb.debian.org/debian unstable/main amd64 libprotoc32t64 amd64 3.21.12-10+b1 [920 kB] Get: 307 http://deb.debian.org/debian unstable/main amd64 libprotoc-dev amd64 3.21.12-10+b1 [1023 kB] Get: 308 http://deb.debian.org/debian unstable/main amd64 libyajl2 amd64 2.1.0-5+b2 [23.3 kB] Get: 309 http://deb.debian.org/debian unstable/main amd64 libraptor2-0 amd64 2.0.16-4+b1 [177 kB] Get: 310 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [795 kB] Get: 311 http://deb.debian.org/debian unstable/main amd64 libxslt1-dev amd64 1.1.35-1.1+b1 [346 kB] Get: 312 http://deb.debian.org/debian unstable/main amd64 libyajl-dev amd64 2.1.0-5+b2 [32.0 kB] Get: 313 http://deb.debian.org/debian unstable/main amd64 libraptor2-dev amd64 2.0.16-4+b1 [211 kB] Get: 314 http://deb.debian.org/debian unstable/main amd64 librasqal3t64 amd64 0.9.33-2.1+b2 [191 kB] Get: 315 http://deb.debian.org/debian unstable/main amd64 librasqal3-dev amd64 0.9.33-2.1+b2 [227 kB] Get: 316 http://deb.debian.org/debian unstable/main amd64 librdf0t64 amd64 1.0.17-4+b1 [107 kB] Get: 317 http://deb.debian.org/debian unstable/main amd64 librdf0-dev amd64 1.0.17-4+b1 [238 kB] Get: 318 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.2-1 [465 kB] Get: 319 http://deb.debian.org/debian unstable/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12+b2 [36.8 kB] Get: 320 http://deb.debian.org/debian unstable/main amd64 libsmithwaterman-dev amd64 0.0+git20160702.2610e25-12+b2 [41.4 kB] Get: 321 http://deb.debian.org/debian unstable/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 322 http://deb.debian.org/debian unstable/main amd64 libssw0 amd64 1.1-15+b1 [21.8 kB] Get: 323 http://deb.debian.org/debian unstable/main amd64 libssw-dev amd64 1.1-15+b1 [24.6 kB] Get: 324 http://deb.debian.org/debian unstable/main amd64 libtabixpp0t64 amd64 1.1.2-2.1+b1 [10.3 kB] Get: 325 http://deb.debian.org/debian unstable/main amd64 libtabixpp-dev amd64 1.1.2-2.1+b1 [9528 B] Get: 326 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get: 327 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get: 328 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get: 329 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get: 330 http://deb.debian.org/debian unstable/main amd64 libtsl-hopscotch-map-dev all 2.3.1-1 [36.6 kB] Get: 331 http://deb.debian.org/debian unstable/main amd64 libwfa2-0 amd64 2.3.3-4+b1 [61.1 kB] Get: 332 http://deb.debian.org/debian unstable/main amd64 libvcflib2 amd64 1.0.9+dfsg1-3+b2 [194 kB] Get: 333 http://deb.debian.org/debian unstable/main amd64 libwfa2-dev amd64 2.3.3-4+b1 [79.7 kB] Get: 334 http://deb.debian.org/debian unstable/main amd64 libvcflib-dev amd64 1.0.9+dfsg1-3+b2 [77.8 kB] Get: 335 http://deb.debian.org/debian unstable/main amd64 zip amd64 3.0-14 [233 kB] Get: 336 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB] Get: 337 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 338 http://deb.debian.org/debian unstable/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Get: 339 http://deb.debian.org/debian unstable/main amd64 r-cran-littler amd64 0.3.20-1 [102 kB] Get: 340 http://deb.debian.org/debian unstable/main amd64 littler all 0.3.20-1 [16.0 kB] Get: 341 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get: 342 http://deb.debian.org/debian unstable/main amd64 r-cran-rcpp amd64 1.0.13-1-1 [2074 kB] Get: 343 http://deb.debian.org/debian unstable/main amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] Get: 344 http://deb.debian.org/debian unstable/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB] Get: 345 http://deb.debian.org/debian unstable/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get: 346 http://deb.debian.org/debian unstable/main amd64 r-cran-rlang amd64 1.1.4-1 [1712 kB] Get: 347 http://deb.debian.org/debian unstable/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get: 348 http://deb.debian.org/debian unstable/main amd64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Get: 349 http://deb.debian.org/debian unstable/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get: 350 http://deb.debian.org/debian unstable/main amd64 r-cran-mass amd64 7.3-61-1 [1112 kB] Get: 351 http://deb.debian.org/debian unstable/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get: 352 http://deb.debian.org/debian unstable/main amd64 r-cran-nlme amd64 3.1.166-1 [2330 kB] Get: 353 http://deb.debian.org/debian unstable/main amd64 r-cran-matrix amd64 1.7-1-1 [4138 kB] Get: 354 http://deb.debian.org/debian unstable/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get: 355 http://deb.debian.org/debian unstable/main amd64 r-cran-farver amd64 2.1.2-1 [1411 kB] Get: 356 http://deb.debian.org/debian unstable/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get: 357 http://deb.debian.org/debian unstable/main amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1716 kB] Get: 358 http://deb.debian.org/debian unstable/main amd64 r-cran-munsell all 0.5.1-1 [237 kB] Get: 359 http://deb.debian.org/debian unstable/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get: 360 http://deb.debian.org/debian unstable/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get: 361 http://deb.debian.org/debian unstable/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get: 362 http://deb.debian.org/debian unstable/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get: 363 http://deb.debian.org/debian unstable/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get: 364 http://deb.debian.org/debian unstable/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get: 365 http://deb.debian.org/debian unstable/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get: 366 http://deb.debian.org/debian unstable/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get: 367 http://deb.debian.org/debian unstable/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get: 368 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 369 http://deb.debian.org/debian unstable/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get: 370 http://deb.debian.org/debian unstable/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get: 371 http://deb.debian.org/debian unstable/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get: 372 http://deb.debian.org/debian unstable/main amd64 r-cran-gridbase all 0.4-7-5 [163 kB] Get: 373 http://deb.debian.org/debian unstable/main amd64 libvcflib-tools amd64 1.0.9+dfsg1-3+b2 [660 kB] Get: 374 http://deb.debian.org/debian unstable/main amd64 protobuf-compiler amd64 3.21.12-10+b1 [84.8 kB] Get: 375 http://deb.debian.org/debian unstable/main amd64 pv amd64 1.9.0-1 [93.0 kB] Get: 376 http://deb.debian.org/debian unstable/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Get: 377 http://deb.debian.org/debian unstable/main amd64 raptor2-utils amd64 2.0.16-4+b1 [35.0 kB] Get: 378 http://deb.debian.org/debian unstable/main amd64 rasqal-utils amd64 0.9.33-2.1+b2 [43.8 kB] Get: 379 http://deb.debian.org/debian unstable/main amd64 rs amd64 20200313-1 [15.5 kB] Get: 380 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.20-3 [653 kB] Get: 381 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.20+ds-2 [486 kB] Get: 382 http://deb.debian.org/debian unstable/main amd64 xxd amd64 2:9.1.0861-1 [98.1 kB] Fetched 265 MB in 19s (13.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package m4. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19966 files and directories currently installed.) Preparing to unpack .../archives/m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package flex. Preparing to unpack .../flex_2.6.4-8.2+b3_amd64.deb ... Unpacking flex (2.6.4-8.2+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../libsigsegv2_2.14-1+b2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.14-1+b2) ... Setting up readline-common (8.2-5) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up libsigsegv2:amd64 (2.14-1+b2) ... 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 ... 20191 files and directories currently installed.) Preparing to unpack .../0-gawk_1%3a5.2.1-2+b1_amd64.deb ... Unpacking gawk (1:5.2.1-2+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../1-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package ucf. Preparing to unpack .../2-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package libdebuginfod-common. Preparing to unpack .../3-libdebuginfod-common_0.192-4_all.deb ... Unpacking libdebuginfod-common (0.192-4) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../4-liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../5-libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../6-libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../7-python3.12-minimal_3.12.7-3_amd64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:amd64 (3.12.7-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... 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 ... 20801 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_amd64.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../13-libpython3.12-stdlib_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../14-python3.12_3.12.7-3_amd64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../15-libpython3-stdlib_3.12.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21831 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.7-1_amd64.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-6_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-6_amd64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.3.2-2_amd64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../007-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. 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Setting up libmount-dev:amd64 (2.40.2-11) ... Setting up libclang-cpp19 (1:19.1.3-2) ... Setting up libgnutls28-dev:amd64 (3.8.8-2) ... Setting up libpaper1:amd64 (1.1.29+b2) ... Creating config file /etc/papersize with new version Setting up libnghttp2-dev:amd64 (1.64.0-1) ... Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up libavif16:amd64 (1.1.1-1) ... Setting up libxft2:amd64 (2.3.6-1+b2) ... Setting up libgio-2.0-dev:amd64 (2.82.2-3) ... Setting up girepository-tools:amd64 (2.82.2-3) ... Setting up libxcb1-dev:amd64 (1.17.0-2+b1) ... Setting up libxslt1-dev:amd64 (1.1.35-1.1+b1) ... Setting up libdebuginfod-common (0.192-4) ... Setting up libcurl4t64:amd64 (8.11.0-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up libsm-dev:amd64 (2:1.2.4-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:amd64 (8.6.15-1) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ... Setting up xsltproc (1.1.35-1.1+b1) ... Setting up libx11-dev:amd64 (2:1.8.10-2) ... Setting up libcurl3t64-gnutls:amd64 (8.11.0-1) ... Setting up libpaper-utils (1.1.29+b2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libdw-dev:amd64 (0.192-4) ... Setting up libcairo2:amd64 (1.18.2-2) ... Setting up libfreetype-dev:amd64 (2.13.3+dfsg-1) ... Setting up libxcb-shm0-dev:amd64 (1.17.0-2+b1) ... Setting up doxygen (1.9.8+ds-2+b3) ... Setting up libgssrpc4t64:amd64 (1.21.3-3) ... Setting up libraqm0:amd64 (0.10.1-1+b2) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b1) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libxcb-render0-dev:amd64 (1.17.0-2+b1) ... Setting up libxext-dev:amd64 (2:1.3.4-1+b2) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up cmake (3.31.1-1) ... Setting up libhts3t64:amd64 (1.20+ds-2) ... Setting up libcairo-gobject2:amd64 (1.18.2-2) ... Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libxrender-dev:amd64 (1:0.9.10-1.1+b2) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-3) ... Setting up libcairo-script-interpreter2:amd64 (1.18.2-2) ... Setting up libdebuginfod1t64:amd64 (0.192-4) ... Setting up libxmu6:amd64 (2:1.1.3-3+b3) ... Setting up libpython3.12-stdlib:amd64 (3.12.7-3) ... Setting up libkdb5-10t64:amd64 (1.21.3-3) ... Setting up libfontconfig-dev:amd64 (2.15.0-1.1+b1) ... Setting up python3.12 (3.12.7-3) ... Setting up libraptor2-0:amd64 (2.0.16-4+b1) ... Setting up raptor2-utils (2.0.16-4+b1) ... Setting up debhelper (13.20) ... Setting up librasqal3t64:amd64 (0.9.33-2.1+b2) ... Setting up libxaw7:amd64 (2:1.0.16-1) ... Setting up librdf0t64:amd64 (1.0.17-4+b1) ... Setting up samtools (1.20-3) ... Setting up r-base-core (4.4.2-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-labeling (0.4.3-1) ... Setting up r-cran-lattice (0.22-6-1) ... Setting up r-cran-nlme (3.1.166-1) ... Setting up r-cran-farver (2.1.2-1) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-3) ... Setting up libtabixpp0t64:amd64 (1.1.2-2.1+b1) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.4-1) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up libpython3-stdlib:amd64 (3.12.7-1) ... Setting up krb5-multidev:amd64 (1.21.3-3) ... Setting up r-cran-littler (0.3.20-1) ... Setting up r-cran-rcpp (1.0.13-1-1) ... Setting up rasqal-utils (0.9.33-2.1+b2) ... Setting up elfutils (0.192-4) ... Setting up r-cran-rlang (1.1.4-1) ... Setting up r-cran-gridbase (0.4-7-5) ... Setting up littler (0.3.20-1) ... Setting up r-cran-withr (3.0.2+dfsg-1) ... Setting up r-cran-fansi (1.0.5-1) ... Setting up r-cran-mass (7.3-61-1) ... Setting up python3 (3.12.7-1) ... /usr/share/gtk-doc/python/gtkdoc/scan.py:44: SyntaxWarning: invalid escape sequence '\s' VAR_TYPE_MODIFIER = '(?:' + '|'.join([t + '\s+' for t in TYPE_MODIFIERS]) + ')*' /usr/share/gtk-doc/python/gtkdoc/scan.py:45: SyntaxWarning: invalid escape sequence '\s' RET_TYPE_MODIFIER = '(?:' + '|'.join([t + '\s+' for t in TYPE_MODIFIERS + ['G_CONST_RETURN']]) + ')*' /usr/share/gtk-doc/python/gtkdoc/scan.py:238: SyntaxWarning: invalid escape sequence '\(' ignore_decorators = '|' + options.ignore_decorators.replace('()', '\(\w*\)') /usr/share/gtk-doc/python/gtkdoc/scan.py:239: SyntaxWarning: invalid escape sequence '\s' optional_decorators_regex = '(?:\s+(?:%s))?' % ignore_decorators[1:] /usr/share/gtk-doc/python/gtkdoc/scan.py:487: SyntaxWarning: invalid escape sequence '\(' ignore_decorators = '|' + options.ignore_decorators.replace('()', '\(\w*\)') /usr/share/gtk-doc/python/gtkdoc/scan.py:488: SyntaxWarning: invalid escape sequence '\s' optional_decorators_regex = '(?:\s+(?:%s))?' % ignore_decorators[1:] Setting up python3-autocommand (2.2.2-3) ... Setting up r-cran-glue (1.7.0-1) ... Setting up r-cran-cli (3.6.3-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up libkrb5-dev:amd64 (1.21.3-3) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up python3-packaging (24.2-1) ... Setting up r-cran-colorspace (2.1-1+dfsg-1) ... Setting up libvcflib2:amd64 (1.0.9+dfsg1-3+b2) ... Setting up r-cran-plyr (1.8.9-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up r-cran-gtable (0.3.6+dfsg-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up r-cran-matrix (1.7-1-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up python3-lxml:amd64 (5.3.0-1+b1) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up libgio-2.0-dev-bin (2.82.2-3) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up r-cran-munsell (0.5.1-1) ... Setting up r-cran-tibble (3.2.1+dfsg-2) ... Setting up libcurl4-gnutls-dev:amd64 (8.11.0-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up r-cran-scales (1.3.0-1) ... Setting up libraptor2-dev:amd64 (2.0.16-4+b1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up libglib2.0-dev-bin (2.82.2-3) ... Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... Setting up libhts-dev:amd64 (1.20+ds-2) ... Setting up librasqal3-dev (0.9.33-2.1+b2) ... Setting up libvcflib-tools (1.0.9+dfsg1-3+b2) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up libglib2.0-dev:amd64 (2.82.2-3) ... Setting up librdf0-dev (1.0.17-4+b1) ... Setting up libtabixpp-dev:amd64 (1.1.2-2.1+b1) ... Setting up libcairo2-dev:amd64 (1.18.2-2) ... Setting up libvcflib-dev:amd64 (1.0.9+dfsg1-3+b2) ... Setting up libheif-plugin-dav1d:amd64 (1.19.3-1) ... Setting up libheif-plugin-libde265:amd64 (1.19.3-1) ... Setting up libheif1:amd64 (1.19.3-1) ... Setting up libgd3:amd64 (2.3.3-12+b1) ... Setting up libgvc6 (2.42.4-2+b1) ... Setting up graphviz (2.42.4-2+b1) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-xsl (1.79.2+dfsg-7) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-xml (4.5-13) ... Setting up docbook (4.5-11) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-to-man (1:2.0.0-47) ... Setting up gtk-doc-tools (1.34.0-1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/vg-1.59.0+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_1.59.0+ds-0.1_source.changes dpkg-buildpackage: info: source package vg dpkg-buildpackage: info: source version 1.59.0+ds-0.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Bastian Germann dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' find /build/reproducible-path/vg-1.59.0+ds/include/ -type f -a '!' -name vg_git_version.hpp -delete dh_auto_clean || true make -j42 clean make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC CXXFLAGS are -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp LDFLAGS are -Wl,-z,relro -Wl,-z,now rm -f -r bin/unittest rm -f -r lib rm -f -r obj/unittest/support rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/pic/io rm -f -r obj/io rm -f -r obj/pic/algorithms rm -f -r obj/algorithms rm -f -r obj/config rm -f -r obj/pic rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd C && make clean cd externalTools && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make clean cd quicktree_1.1 && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' rm -rf ../bin ../lib make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/gcsa2' make[2]: *** [Makefile:854: clean] Error 2 make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_clean: error: make -j42 clean returned exit code 2 make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' rm -Rf ./deps/DYNAMIC/build/CMakeFiles dh_clean make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' dh_autoreconf --sourcedirectory=/build/reproducible-path/vg-1.59.0+ds/deps/vowpal_wabbit make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_configure debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' mkdir -p /build/reproducible-path/vg-1.59.0+ds/debian/help find . -type d -name simde | xargs rm -Rf mkdir -p /build/reproducible-path/vg-1.59.0+ds/debian/vg/usr mkdir -p /build/reproducible-path/vg-1.59.0+ds/debian/vg/usr/lib/vg for SIMD in avx2 avx sse4.1 ssse3 sse3 ; do \ export CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -m${SIMD}" && export CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -m${SIMD}" && \ make clean ; \ dh_auto_build -- SFX=-${SIMD} all test/build_graph bin/shuf ; \ done make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC CXXFLAGS are -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp LDFLAGS are -Wl,-z,relro -Wl,-z,now rm -f -r bin/unittest rm -f -r lib rm -f -r obj/unittest/support rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/pic/io rm -f -r obj/io rm -f -r obj/pic/algorithms rm -f -r obj/algorithms rm -f -r obj/config rm -f -r obj/pic rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/gcsa2' make[2]: *** [Makefile:854: clean] Error 2 make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' make -j42 "INSTALL=install --strip-program=true" SFX=-avx2 all test/build_graph bin/shuf make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC CXXFLAGS are -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp LDFLAGS are -Wl,-z,relro -Wl,-z,now . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" ./install.sh /build/reproducible-path/vg-1.59.0+ds . ./source_me.sh && cd deps/ssw/src && make && ar rs /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a ssw.o ssw_cpp.o && cp ssw_cpp.h ssw.h /build/reproducible-path/vg-1.59.0+ds/include . ./source_me.sh && cd deps/libhandlegraph && rm -Rf build CMakeCache.txt CMakeFiles && mkdir build && cd build && CXXFLAGS="-std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make && make install . ./source_me.sh && cd deps/kff-cpp-api && rm -Rf build && mkdir build && cd build && cmake .. && make && cp kff_io.hpp /build/reproducible-path/vg-1.59.0+ds/include && mv libkff.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && cd deps/gssw && make && cp lib/libgssw.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp src/gssw.h /build/reproducible-path/vg-1.59.0+ds/include/ . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/reproducible-path/vg-1.59.0+ds/include" make libs && cp lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/lib/ && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS && cp src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp -r src/include/structures /build/reproducible-path/vg-1.59.0+ds/include/ rm -f lib/cleaned_old_protobuf* cp deps/BBHash/BooPHF.h /build/reproducible-path/vg-1.59.0+ds/include rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' gcc -c -o ssw.o ssw.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. cp -r deps/sparsepp/sparsepp include/ g++ -c -o ssw_cpp.o ssw_cpp.cpp -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. rm -Rf include/dynamic.hpp include/dynamic make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' gcc -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c rm -Rf include/google/protobuf deps/protobuf Library will be installed in '/build/reproducible-path/vg-1.59.0+ds' gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c # annoyingly doesn't have an install option on the cmake, so we manually move their external dependency headers make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd externalTools && make all cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ touch lib/cleaned_old_protobuf_v003 cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC && rm -Rf build && mkdir -p build && cd build && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" && cmake -DCMAKE_VERBOSE_MAKEFILE=ON .. && make make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make all cd quicktree_1.1 && make all CC="gcc -std=c99" WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. . ./source_me.sh && cp -r deps/mio/include/mio /build/reproducible-path/vg-1.59.0+ds/include/ . ./source_me.sh && cp -r deps/atomic_queue/include/atomic_queue/* /build/reproducible-path/vg-1.59.0+ds/include/ rm -f /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/* make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' . ./source_me.sh && cp -r deps/ips4o/ips4o* /build/reproducible-path/vg-1.59.0+ds/include/ gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c if [ ! -d obj ]; then mkdir -p obj; fi make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' cd ./deps/lru_cache && cp *.h* /build/reproducible-path/vg-1.59.0+ds/include/ make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c cp deps/sha1/*.h* /build/reproducible-path/vg-1.59.0+ds/include/ cp deps/progress_bar/progress_bar.hpp /build/reproducible-path/vg-1.59.0+ds/include gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' if [ ! -d lib ]; then mkdir -p lib; fi gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/dozeu && cp deps/dozeu/*.h /build/reproducible-path/vg-1.59.0+ds/include/dozeu/ gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj; fi gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o find bin obj lib -type f -delete gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Setting build type to 'Release' as none was specified. if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test; fi make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. if [ ! -d bin ]; then mkdir -p bin; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o if [ ! -d lib ]; then mkdir -p lib; fi if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib; fi . ./source_me.sh && g++ -I -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/progress_bar.o deps/progress_bar/progress_bar.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/union_find.cpp -o obj/union_find.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o ln -s `which shuf` bin/shuf g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o diff: include/vg_environment_version.hpp: No such file or directory g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o . ./source_me.sh && cp deps/mmmultimap/src/mmmultimap.hpp deps/mmmultimap/src/mmmultiset.hpp /build/reproducible-path/vg-1.59.0+ds/include/ ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./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 , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -- The C compiler identification is GNU 14.2.0 ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -- The C compiler identification is GNU 14.2.0 -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- The C compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- The CXX compiler identification is GNU 14.2.0 ar rc cuTest.a *.o -- Detecting C compiler ABI info ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' -- Detecting C compiler ABI info - done -- Detecting C compiler ABI info - done -- Detecting CXX compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info -- Detecting C compiler ABI info -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ -- Detecting CXX compiler ABI info - done -- Detecting CXX compiler ABI info - done -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting CXX compiler ABI info - done libhandlegraph is root project or external_project-- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Configuring done (1.9s) -- Detecting CXX compile features -- Detecting CXX compile features - done -- Compiler is recent enough to support C++14. -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG -- Configuring done (1.9s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build -- Generating done (0.0s) make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks Building in Release mode -- Configuring done (2.0s) make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend src/gssw.c: In function ‘gssw_graph_print’: src/gssw.c:1947:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1947 | fprintf(stdout, "GRAPH // node %llu %u %s\n", n->id, n->len, n->seq); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" src/gssw.c:1951:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1951 | fprintf(stdout, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c:1951:56: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1951 | fprintf(stdout, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c: In function ‘gssw_graph_print_stderr’: src/gssw.c:1963:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1963 | fprintf(stderr, "GRAPH // node %llu %u %s\n", n->id, n->len, n->seq); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c:1967:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1967 | fprintf(stderr, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c:1967:56: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1967 | fprintf(stderr, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c: In function ‘gssw_graph_print_score_matrices’: src/gssw.c:1978:31: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1978 | fprintf(out, "node %llu\n", n->id); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -- Generating done (0.1s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' src/gssw.c: In function ‘gssw_print_graph_cigar’: src/gssw.c:3623:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 3623 | fprintf(out, "%llu[", nc->node->id); | ~~~^ ~~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC -B/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build --check-build-system CMakeFiles/Makefile.cmake 0 src/gssw.c: In function ‘gssw_create_seed_byte’: make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' src/gssw.c:5095:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5095 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); | ~~~^ ~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' src/gssw.c: In function ‘gssw_create_seed_word’: src/gssw.c:5130:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5130 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); | ~~~^ ~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu [ 2%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp [ 5%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o [ 8%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dfs.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/handle_graph.cpp [ 11%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_metadata.cpp [ 14%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build//CMakeFiles/progress.marks /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 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'/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles/wm_string.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build 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object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/copy_graph.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/debug.dir/build.make CMakeFiles/debug.dir/build make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/DYNAMIC/build' /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT 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'/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG - Success make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/DYNAMIC/build' /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong 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-I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_tips.cpp /usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 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CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/topological_sort.cpp [ 57%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 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CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/count_walks.cpp -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success 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 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' [ 65%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -MF 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CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp -- Performing Test HAVE_CXA_DEMANGLE [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dijkstra.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o cd C && make all /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_acyclic.cpp make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+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 -- Performing Test HAVE_CXA_DEMANGLE - Success cp inc/commonC.h ../lib/commonC.h.tmp -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h 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 cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h [ 82%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/reverse_complement.cpp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp [ 85%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/split_strands.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 cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h [ 88%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/chop.cpp 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 cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp [ 91%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:102 (message): git not found. Cloning of submodules will not work. cp inc/stSafeC.h ../lib/stSafeC.h.tmp -- Looking for C++ include cstdio mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp 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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -I inc -I ../lib/ -c impl/*.c [ 94%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/extend.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Looking for C++ include cstdio - found -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -- Configuring done (8.7s) gcc -o ssw_test ssw.o main.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. -lm -lz gcc -o example_c ssw.o example.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. -lm -lz g++ -o example_cpp example.cpp ssw.o ssw_cpp.o -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. -lm -lz cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -- Generating done (0.6s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 8 src/gssw.c: In function ‘gssw_sw_software_byte’: src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 277 | memcpy(scratch, to_unswizzle, size); | ^ In function ‘unswizzle_byte’, inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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)) { | ^ make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bits.cpp [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/config.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_isa.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_config.cpp [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/io.cpp [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/memory_management.cpp [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/louds_tree.cpp [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_fs.cpp make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' ar: creating /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sd_vector.cpp [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sfstream.cpp src/gssw.c: In function ‘gssw_sw_software_word’: src/gssw.c:1117:5: warning: ‘__builtin_memcpy’ writing between 18446744069414584336 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 1117 | memcpy(scratch, to_unswizzle, size * sizeof(int16_t)); | ^ In function ‘unswizzle_word’, inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o -MF CMakeFiles/sdsl.dir/simple_sds.cpp.o.d -o CMakeFiles/sdsl.dir/simple_sds.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/simple_sds.cpp [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/structure_tree.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint128_t.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/vector:63, from /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:8: In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = long int]’, inlined from ‘static void std::allocator_traits >::deallocate(allocator_type&, pointer, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:544:23, inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:389:19, inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:368:15, inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:738:7, inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:445:5: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: ‘void operator delete(void*, std::size_t)’ called on pointer ‘’ with nonzero offset [1, 9223372036854775800] [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = long int]’, inlined from ‘static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:509:28, inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:398:44, inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:334:26, inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const value_type&, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:571:47, inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:327:85: /usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from ‘void* operator new(std::size_t)’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/wt_helper.cpp src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4975:5: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 4975 | strncpy(n->seq, seq, len); n->seq[len] = 0; | ^ src/gssw.c:4971:19: note: length computed here 4971 | int32_t len = strlen(seq); | ^~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1358:27, inlined from ‘void sdsl::int_vector< >::resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:380:23, inlined from ‘sdsl::int_vector< >::int_vector(size_type, value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1285:11, inlined from ‘sdsl::excess::impl::impl()’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:448:9: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 448 | *word &= | ^~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 56%] 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 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/debug.dir/link.d CMakeFiles/debug.dir/debug.cpp.o -o debug make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ar rc /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o [ 56%] Built target debug [ 33%] Linking CXX static library libkff.a ranlib /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:765:75: note: declared here 765 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:773:68: note: declared here 773 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:774:68: note: declared here 774 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz ar rvs lib/libgssw.a obj/gssw.o gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' [ 33%] Built target kff make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 50%] Building CXX object CMakeFiles/kff_example.dir/main.cpp.o [ 66%] Building CXX object benchmarks/CMakeFiles/reader_bench.dir/reader.cpp.o impl/sonLibConnectivity.c: In function ‘stConnectivity_addEdge’: impl/sonLibConnectivity.c:248:33: warning: pointer ‘component1’ may be used after ‘free’ [-Wuse-after-free] 248 | connectivity->mergeCallback(connectivity->mergeExtraData, component1, component2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘stConnectedComponent_destruct’, inlined from ‘stConnectivity_addEdge’ at impl/sonLibConnectivity.c:238:3: impl/sonLibConnectivity.c:608:9: note: call to ‘free’ here 608 | free(comp); | ^~~~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' [ 83%] Linking CXX executable reader_bench cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 62%] Linking CXX executable wm_string /usr/bin/cmake -E cmake_link_script CMakeFiles/wm_string.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/wm_string.dir/link.d CMakeFiles/wm_string.dir/wm_string.cpp.o -o wm_string make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 62%] Built target wm_string [ 68%] Linking CXX executable benchmark /usr/bin/cmake -E cmake_link_script CMakeFiles/benchmark.dir/link.txt --verbose=1 [ 83%] Built target reader_bench cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/benchmark.dir/link.d CMakeFiles/benchmark.dir/benchmark.cpp.o -o benchmark make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 68%] Built target benchmark cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Linking CXX executable kff_example 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-1.59.0+ds/deps/kff-cpp-api/build' [ 75%] Linking CXX executable h0_lz77 [100%] Built target kff_example /usr/bin/cmake -E cmake_link_script CMakeFiles/h0_lz77.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/h0_lz77.dir/link.d CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -o h0_lz77 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 75%] Built target h0_lz77 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 81%] Linking CXX executable cw-bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/cw-bwt.dir/link.txt --verbose=1 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 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/cw-bwt.dir/link.d "CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o" -o cw-bwt make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 81%] Built target cw-bwt [ 87%] Linking CXX executable rle_lz77_v1 /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v1.dir/link.txt --verbose=1 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 93%] Linking CXX executable rle_bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_bwt.dir/link.txt --verbose=1 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/rle_bwt.dir/link.d CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -o rle_bwt make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/rle_lz77_v1.dir/link.d CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -o rle_lz77_v1 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 94%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Linking CXX shared library libhandlegraph.so [100%] 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_shared.dir/link.txt --verbose=1 [ 93%] Built target rle_bwt [ 93%] Built target rle_lz77_v1 /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.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 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,--dependency-file,CMakeFiles/handlegraph_shared.dir/link.d -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/dfs.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_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.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/mutable_path_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/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Built target handlegraph_shared 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 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.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_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.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/mutable_path_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/chop.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-1.59.0+ds/deps/libhandlegraph/build' [100%] Linking CXX executable rle_lz77_v2 /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v2.dir/link.txt --verbose=1 [100%] Built target handlegraph_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/rle_lz77_v2.dir/link.d CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -o rle_lz77_v2 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [100%] Built target rle_lz77_v2 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles 0 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 94%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' # Do the copy of the main file last so we can tell if this recipe failed and redo it. # Otherwise we get dynamic.hpp without its deps mkdir -p include/dynamic && cp -r /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include/dynamic/* include/dynamic/ [ 97%] Built target handlegraph_static make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Built target handlegraph_shared make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.a -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_metadata.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_metadata.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_position_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/deletable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/expanding_overlay_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/util.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/buildable_snarl_decomposition.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/trivially_serializable.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/iteratee.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_tips.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/count_walks.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/split_strands.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/eades_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/are_equivalent.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dijkstra.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/append_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/apply_orientations.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal/dfs.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dagify.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/reverse_complement.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_shortest_paths.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/topological_sort.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/copy_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/strongly_connected_components.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/chop.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/extend.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/weakly_connected_components.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_single_stranded.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_acyclic.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/snarl_decomposition.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/types.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/named_node_back_translation.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphConfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphConfigVersion.cmake make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' rm -f /build/reproducible-path/vg-1.59.0+ds/include/vg.pb.h /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" && export LDFLAGS="-Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && rm -rf build-vg && mkdir build-vg && cd build-vg && PKG_CONFIG_PATH=/build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig: cmake -DCMAKE_CXX_STANDARD=14 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH="/usr;/" -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make clean && VERBOSE=1 make && make install cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibTreap.c: In function ‘stTreap_remove’: impl/sonLibTreap.c:331:18: warning: pointer ‘rmnode’ used after ‘free’ [-Wuse-after-free] 331 | stTreap *p = rmnode->parent; | ^ impl/sonLibTreap.c:329:9: note: call to ‘free’ here 329 | free(rmnode); | ^~~~~~~~~~~~ -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done 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 -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") Building libvgio for C++ 14 -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Could NOT find Protobuf (missing: Protobuf_DIR) No installed Protobuf has registered itself with CMake. cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.21.12") Found Protobuf using FindProtobuf.cmake -- Found Threads: TRUE Using real Threads library -- Checking for module 'htslib' -- Found htslib, version 1.20 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Checking for module 'jansson' -- Found jansson, version 2.14 Using installed libhandlegraph -- Configuring done (7.7s) -- Generating done (0.1s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make -f CMakeFiles/test_libvgio.dir/build.make CMakeFiles/test_libvgio.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/test_libvgio.dir/cmake_clean.cmake /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" 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-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 0%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 2%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto [ 5%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 8%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_emitter.cpp [ 11%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o [ 14%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_io.cpp [ 17%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o [ 20%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/vg.pb.cc.o -MF CMakeFiles/vgio_static.dir/vg.pb.cc.o.d -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/vg.pb.cc [ 23%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o [ 26%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o [ 29%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fopenmp -MD -MT 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/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" [ 47%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream_multiplexer.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 52%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o [ 55%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong 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CMakeFiles/vgio.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/basic_stream.cpp [ 58%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o.d -o 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CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/edit.cpp.o -MF CMakeFiles/vgio.dir/src/edit.cpp.o.d -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/edit.cpp /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_io.cpp [ 73%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/hfile_cppstream.cpp [ 76%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/json2pb.cpp [ 79%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_iterator.cpp [ 82%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_emitter.cpp [ 88%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o [ 85%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/registry.cpp.o -MF CMakeFiles/vgio.dir/src/registry.cpp.o.d -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/registry.cpp [ 91%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/stream.cpp.o -MF CMakeFiles/vgio.dir/src/stream.cpp.o.d -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream.cpp /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream_multiplexer.cpp [ 94%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/vpkg.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Linking CXX static library libsdsl.a cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/vg-1.59.0+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/simple_sds.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 /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/reproducible-path/vg-1.59.0+ds/include/sdsl/*' rm -f '/build/reproducible-path/vg-1.59.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib 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/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/config.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/io.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/iterators.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rle_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/simple_sds.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/util.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/vectors.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libsdsl.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/reproducible-path/vg-1.59.0+ds/include'. The library files are located in '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include/ && cd deps/gcsa2 && make directories && make lib/libgcsa2.a && mv lib/libgcsa2.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwt && make clean && make && mv lib/libgbwt.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/reproducible-path/vg-1.59.0+ds/include:/build/reproducible-path/vg-1.59.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" make && cp lib/libbdsg.a /build/reproducible-path/vg-1.59.0+ds/lib && cp -r bdsg/include/* /build/reproducible-path/vg-1.59.0+ds/include rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' mkdir -p bin mkdir -p lib mkdir -p obj make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' rm -rf bin lib obj make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C rm -f *.o *.a build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' rm -f test_bwtmerge test_metadata test_queries test_support test_variants *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' mkdir -p bin mkdir -p lib mkdir -p obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/bwtmerge.o src/bwtmerge.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwt.o src/cached_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dynamic_gbwt.o src/dynamic_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/fast_locate.o src/fast_locate.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude 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-Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata.o src/metadata.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/variants.o src/variants.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_gbwt.o src/build_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_ri.o src/build_ri.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/merge_gbwt.o src/merge_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/benchmark.o src/benchmark.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata_tool.o src/metadata_tool.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp [ ! -e bdsg/obj ] || rm -r bdsg/obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dbg.o src/dbg.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp [ ! -e lib ] || rm -r lib /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gcsa.o src/gcsa.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/lcp.o src/lcp.cpp [ ! -e bin ] || rm -r bin /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_graph.o src/path_graph.cpp make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/mapped_structs.cpp -o bdsg/obj/mapped_structs.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/reference_path_overlay.cpp -o bdsg/obj/reference_path_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/packed_reference_path_overlay.cpp -o bdsg/obj/packed_reference_path_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/path_subgraph_overlay.cpp -o bdsg/obj/path_subgraph_overlay.o 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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/subgraph_overlay.cpp -o bdsg/obj/subgraph_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o 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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest 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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest [ 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 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wl,--dependency-file,CMakeFiles/vgio.dir/link.d -Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib -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 /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [100%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake [100%] Built target vgio /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-1.59.0+ds/deps/libvgio/build-vg' [100%] Built target vgio_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 0%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 50%] Built target vgio_static [100%] Built target vgio make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libvgio.so -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libvgio.a -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/loader.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/json2pb.h -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/registry.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/edit.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' mv ../bin/sonLibTests.tmp ../bin/sonLibTests make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sonLib' . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/reproducible-path/vg-1.59.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/reproducible-path/vg-1.59.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/reproducible-path/vg-1.59.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c ar rc 3EdgeConnected.a *.o 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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I .//../sonLib/lib/ -c impl/*.c gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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 ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' ar rcs lib/libgbwt.a obj/algorithms.o obj/bwtmerge.o obj/cached_gbwt.o obj/dynamic_gbwt.o obj/fast_locate.o obj/files.o obj/gbwt.o obj/internal.o obj/metadata.o obj/support.o obj/test.o obj/utils.o obj/variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_gbwt obj/build_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_ri obj/build_ri.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/merge_gbwt obj/merge_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/benchmark obj/benchmark.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/metadata_tool obj/metadata_tool.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/remove_seq obj/remove_seq.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 rm obj/build_ri.o obj/metadata_tool.o obj/benchmark.o obj/merge_gbwt.o obj/remove_seq.o obj/build_gbwt.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv lib/libgbwtgraph.a /build/reproducible-path/vg-1.59.0+ds/lib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' rm -rf bin lib obj rm -f *.o *.a gfa2gbwt cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' rm -f test_utils test_gbwtgraph test_cached_gbwtgraph test_gfa test_gbz test_minimizer test_index test_algorithms test_path_cover *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' mkdir -p bin mkdir -p lib mkdir -p obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwtgraph.o src/cached_gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwtgraph.o src/gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz.o src/gbz.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa.o src/gfa.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/minimizer.o src/minimizer.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_cover.o src/path_cover.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa2gbwt.o src/gfa2gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz_stats.o src/gbz_stats.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/kmer_freq.o src/kmer_freq.cpp ar rcs lib/libgcsa2.a obj/algorithms.o obj/dbg.o obj/files.o obj/gcsa.o obj/internal.o obj/lcp.o obj/path_graph.o obj/support.o obj/utils.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' 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/mapped_structs.o bdsg/obj/packed_graph.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/reference_path_overlay.o bdsg/obj/packed_reference_path_overlay.o bdsg/obj/path_subgraph_overlay.o bdsg/obj/subgraph_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/snarl_distance_index.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a ar rcs lib/libgbwtgraph.a obj/algorithms.o obj/cached_gbwtgraph.o obj/gbwtgraph.o obj/gbz.o obj/gfa.o obj/internal.o obj/minimizer.o obj/path_cover.o obj/utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/gfa2gbwt obj/gfa2gbwt.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/gbz_stats obj/gbz_stats.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/kmer_freq obj/kmer_freq.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 rm obj/kmer_freq.o obj/gbz_stats.o obj/gfa2gbwt.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/back_translating_alignment_emitter.o src/back_translating_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/clip.o src/clip.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/contracting_graph.o src/contracting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/explainer.o src/explainer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/flat_file_back_translation.o src/flat_file_back_translation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/gbwt_extender.o src/gbwt_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/gbwtgraph_helper.o src/gbwtgraph_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/gcsa_helper.o src/gcsa_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/job_schedule.o src/job_schedule.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/kff.o src/kff.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/kmp.o src/kmp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/mem_accelerator.o src/mem_accelerator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/minimizer_mapper_from_chains.o src/minimizer_mapper_from_chains.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/recombinator.o src/recombinator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/snarl_distance_index.o src/snarl_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/snarl_seed_clusterer.o src/snarl_seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/sparse_union_find.o src/sparse_union_find.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subpath_overlay.o src/subpath_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/traversal_clusters.o src/traversal_clusters.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/zstdutil.o src/zstdutil.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/back_translate.o src/algorithms/back_translate.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/chain_items.o src/algorithms/chain_items.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/component.o src/algorithms/component.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/find_gbwt.o src/algorithms/find_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/find_gbwtgraph.o src/algorithms/find_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/find_translation.o src/algorithms/find_translation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/intersect_path_offsets.o src/algorithms/intersect_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/locally_expand_graph.o src/algorithms/locally_expand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/min_cut_graph.o src/algorithms/min_cut_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/pad_band.o src/algorithms/pad_band.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/prune_to_connecting_graph.o src/algorithms/prune_to_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_params_json.o src/io/register_loader_params_json.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbz.o src/io/register_loader_saver_gbz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbzgraph.o src/io/register_loader_saver_gbzgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gfa.o src/io/register_loader_saver_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/back_translate.o src/unittest/back_translate.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/chain_items.o src/unittest/chain_items.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/component_paths.o src/unittest/component_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/gbwt_extender.o src/unittest/gbwt_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/index_helpers.o src/unittest/index_helpers.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/kff.o src/unittest/kff.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/kmp.o src/unittest/kmp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/locally_expand_graph.o src/unittest/locally_expand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/mem_accelerator.o src/unittest/mem_accelerator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/min_cut_graph.o src/unittest/min_cut_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/protobuf.o src/unittest/protobuf.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/snarl_distance_index.o src/unittest/snarl_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/snarl_seed_clusterer.o src/unittest/snarl_seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/transcriptome.o src/unittest/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/chain_main.o src/subcommand/chain_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/clip_main.o src/subcommand/clip_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/haplotypes_main.o src/subcommand/haplotypes_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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:147:31: required from here 147 | gs.stream_sort(gam_in, cout, index.get()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/any.h:38, from /usr/include/google/protobuf/generated_message_util.h:52, from /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4: /usr/include/google/protobuf/message_lite.h:381:7: note: declared here 381 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/options.o src/subcommand/options.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -MMD -MP -c -o obj/config/allocator_config_jemalloc.o src/config/allocator_config_jemalloc.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/back_translating_alignment_emitter.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/clip.o obj/cluster.o obj/constructor.o obj/contracting_graph.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/explainer.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flat_file_back_translation.o obj/flow_sort.o obj/funnel.o obj/gbwt_extender.o obj/gbwt_helper.o obj/gbwtgraph_helper.o obj/gcsa_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/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/job_schedule.o obj/kff.o obj/kmer.o obj/kmp.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/mem_accelerator.o obj/memoizing_graph.o obj/memusage.o obj/minimizer_mapper.o obj/minimizer_mapper_from_chains.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/recombinator.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarl_distance_index.o obj/snarl_seed_clusterer.o obj/snarls.o obj/source_sink_overlay.o obj/sparse_union_find.o obj/splicing.o obj/split_strand_graph.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/subpath_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_clusters.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/zstdutil.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/back_translate.o obj/algorithms/chain_items.o obj/algorithms/component.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/find_gbwt.o obj/algorithms/find_gbwtgraph.o obj/algorithms/find_translation.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/intersect_path_offsets.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/locally_expand_graph.o obj/algorithms/merge.o obj/algorithms/min_cut_graph.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/pad_band.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/prune_to_connecting_graph.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/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_params_json.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_gbz.o obj/io/register_loader_saver_gbzgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_gfa.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_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++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -o test/build_graph test/build_graph.cpp -Wl,-z,relro -Wl,-z,now lib/libvg.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph -lfastahack -lhts -ltabixpp -lcairo -lm -ldl -lz -lz -lm -lz -lfontconfig -lz -lz -lm -lz -lbrotlicommon -lexpat -lm -lfreetype -lz -lbz2 -lpng16 -lz -lm -lz -lbrotlidec -lbrotlicommon -lX11 -lpthread -lxcb -lXau -lXext -lpthread -lxcb -lXau -lXrender -lX11 -lpthread -lxcb -lXau -lX11 -lpthread -lXau -lxcb -lXau -lxcb-render -lxcb -lXau -lxcb-shm -lxcb -lXau -lXdmcp -lpixman-1 -lm -pthread -lzstd -pthread -rdynamic -ldw -lelf -latomic "-lboost_program_options""" -ldl -llzma -lzstd /usr/lib/x86_64-linux-gnu/libjemalloc.a -Wl,-Bstatic -lvgio -lhts -ldeflate -lz -llzma -lprotobuf -lz -ljansson -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -o bin/vg-avx2 obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/back_translate.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/chain_items.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/component_paths.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/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gbwt_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_helpers.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/kff.o obj/unittest/kmp.o obj/unittest/locally_expand_graph.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/mem_accelerator.o obj/unittest/min_cut_graph.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/protobuf.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/sequence_complexity.o obj/unittest/snarl_distance_index.o obj/unittest/snarl_seed_clusterer.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.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/transcriptome.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/chain_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/clip_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/haplotypes_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/options.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_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/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 obj/config/allocator_config_jemalloc.o -Wl,-z,relro -Wl,-z,now lib/libvg.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph -lfastahack -lhts -ltabixpp -lcairo -lm -ldl -lz -lz -lm -lz -lfontconfig -lz -lz -lm -lz -lbrotlicommon -lexpat -lm -lfreetype -lz -lbz2 -lpng16 -lz -lm -lz -lbrotlidec -lbrotlicommon -lX11 -lpthread -lxcb -lXau -lXext -lpthread -lxcb -lXau -lXrender -lX11 -lpthread -lxcb -lXau -lX11 -lpthread -lXau -lxcb -lXau -lxcb-render -lxcb -lXau -lxcb-shm -lxcb -lXau -lXdmcp -lpixman-1 -lm -pthread -lzstd -pthread -rdynamic -ldw -lelf -latomic "-lboost_program_options""" -ldl -llzma -lzstd /usr/lib/x86_64-linux-gnu/libjemalloc.a -Wl,-Bstatic -lvgio -lhts -ldeflate -lz -llzma -lprotobuf -lz -ljansson -Wl,-Bdynamic -lpthread -lm make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC CXXFLAGS are -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp LDFLAGS are -Wl,-z,relro -Wl,-z,now rm -f -r bin/unittest rm -f -r lib rm -f -r obj/unittest/support rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/pic/io rm -f -r obj/io rm -f -r obj/pic/algorithms rm -f -r obj/algorithms rm -f -r obj/config rm -f -r obj/pic rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' rm -rf bin lib obj rm -f *.o *.a build_gcsa convert_graph gcsa_format try_extend cd benchmark && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2/benchmark' rm -f count_kmers query_gcsa csa_builder csa_query *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2/benchmark' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' rm -rf bin lib obj rm -f *.o *.a build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' rm -f test_bwtmerge test_metadata test_queries test_support test_variants *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' rm -rf bin lib obj rm -f *.o *.a gfa2gbwt cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' rm -f test_utils test_gbwtgraph test_cached_gbwtgraph test_gfa test_gbz test_minimizer test_index test_algorithms test_path_cover *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' cd ./deps && cd kff-cpp-api && rm -Rf build cd ./deps && cd gssw && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' cd ./deps && cd ssw && cd src && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' rm -f ssw.o ssw_cpp.o ssw_test libssw.so example_c example_cpp libsswjni.so ssw.jar ssw/Aligner.class ssw/Alignment.class ssw/Example.class *~ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/progress_bar' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/nonexistent/first-build/lib' and '/nonexistent/first-build/include' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake "--color=" make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -P /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vectors.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bits.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_g.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_comma.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/config.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_bwt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_config.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_isa.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_wt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_fully.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_iterators.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sct3.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/dac_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/enc_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/fast_cache.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/hyb_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/io.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/iterators.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_byte.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_dac.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_wt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/louds_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/memory_management.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/qsufsort.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_fs.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/raster_img.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rle_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sd_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_scan.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sfstream.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/simple_sds.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/structure_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_trees.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint128_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint256_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uintx_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/util.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/vectors.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/vlc_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wm_int.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_ap.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_blcd.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_gmr.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_huff.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_hutu.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_int.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_pc.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/lib/libsdsl.a" - not found -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vector_il.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vectors.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bits.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_g.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_gg.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_comma.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_delta.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_gamma.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_fibonacci.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/config.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_bwt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_config.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_isa.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa_se.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_alphabet_strategy.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_bitcompressed.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sampling_strategy.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_wt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_fully.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_iterators.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sct3.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/dac_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/enc_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/fast_cache.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/hyb_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_buffer.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_io_wrappers.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_mapper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/inv_perm_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/io.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/iterators.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_bitcompressed.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_byte.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_dac.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree2.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_vlc.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_wt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/louds_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/memory_management.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/nn_dict_dynamic.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/qsufsort.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_filebuf.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_fs.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_scan.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v5.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/raster_img.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rle_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sct.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support_sparse_table.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector_15.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sd_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sdsl_concepts.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_mcl.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_scan.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sfstream.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/simple_sds.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_int_stack.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_multi_stack_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_stack_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/structure_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_arrays.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_trees.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint128_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint256_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uintx_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/util.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/vectors.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/vlc_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wavelet_trees.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wm_int.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_ap.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_blcd.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_gmr.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_huff.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_hutu.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_int.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_pc.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_rlmn.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd sha1 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' rm -f /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && rm -Rf build CMakeCache.txt CMakeFiles cd ./deps && cd libvgio && rm -Rf build CMakeCache.txt CMakeFiles # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' make -j42 "INSTALL=install --strip-program=true" SFX=-avx all test/build_graph bin/shuf make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC CXXFLAGS are -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp LDFLAGS are -Wl,-z,relro -Wl,-z,now . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp" ./install.sh /build/reproducible-path/vg-1.59.0+ds . ./source_me.sh && cd deps/ssw/src && make && ar rs /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a ssw.o ssw_cpp.o && cp ssw_cpp.h ssw.h /build/reproducible-path/vg-1.59.0+ds/include . ./source_me.sh && cd deps/libhandlegraph && rm -Rf build CMakeCache.txt CMakeFiles && mkdir build && cd build && CXXFLAGS="-std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make && make install . ./source_me.sh && cd deps/kff-cpp-api && rm -Rf build && mkdir build && cd build && cmake .. && make && cp kff_io.hpp /build/reproducible-path/vg-1.59.0+ds/include && mv libkff.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && cd deps/gssw && make && cp lib/libgssw.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp src/gssw.h /build/reproducible-path/vg-1.59.0+ds/include/ . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/reproducible-path/vg-1.59.0+ds/include" make libs && cp lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/lib/ && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS && cp src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp -r src/include/structures /build/reproducible-path/vg-1.59.0+ds/include/ rm -f lib/cleaned_old_protobuf* rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' rm -f /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g -c -o obj/gssw.o src/gssw.c Library will be installed in '/build/reproducible-path/vg-1.59.0+ds' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd externalTools && make all rm -Rf include/google/protobuf deps/protobuf make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' gcc -c -o ssw.o ssw.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -pipe -O3 -I. g++ -c -o ssw_cpp.o ssw_cpp.cpp -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -pipe -O3 -I. gcc -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj; fi make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make all g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o cd quicktree_1.1 && make all CC="gcc -std=c99" g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o touch lib/cleaned_old_protobuf_v003 make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o if [ ! -d bin ]; then mkdir -p bin; fi cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib; fi gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o if [ ! -d lib ]; then mkdir -p lib; fi make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o find bin obj lib -type f -delete gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o . ./source_me.sh && g++ -I -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/progress_bar.o deps/progress_bar/progress_bar.cpp gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c make[2]: 'bin/shuf' is up to date. 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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/union_find.cpp -o obj/union_find.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/stable_double.cpp -o obj/stable_double.o CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ ./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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- The C compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' -- Detecting C compiler ABI info - done /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info src/gssw.c: In function ‘gssw_graph_print’: src/gssw.c:1947:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1947 | fprintf(stdout, "GRAPH // node %llu %u %s\n", n->id, n->len, n->seq); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c:1951:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1951 | fprintf(stdout, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c:1951:56: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1951 | fprintf(stdout, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c: In function ‘gssw_graph_print_stderr’: src/gssw.c:1963:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1963 | fprintf(stderr, "GRAPH // node %llu %u %s\n", n->id, n->len, n->seq); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c:1967:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1967 | fprintf(stderr, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c:1967:56: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1967 | fprintf(stderr, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c: In function ‘gssw_graph_print_score_matrices’: src/gssw.c:1978:31: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1978 | fprintf(out, "node %llu\n", n->id); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c: In function ‘gssw_print_graph_cigar’: src/gssw.c:3623:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 3623 | fprintf(out, "%llu[", nc->node->id); | ~~~^ ~~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu -- Detecting CXX compiler ABI info - done src/gssw.c: In function ‘gssw_create_seed_byte’: src/gssw.c:5095:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5095 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); | ~~~^ ~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c: In function ‘gssw_create_seed_word’: src/gssw.c:5130:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5130 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); | ~~~^ ~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done (1.5s) -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build -- Compiler is recent enough to support C++14. -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -- Detecting CXX compiler ABI info - done make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features [ 16%] Building CXX object CMakeFiles/kff.dir/kff_io.cpp.o -- Detecting CXX compile features - done libhandlegraph is root project or external_project -- Configuring done (1.5s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS [ 11%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o [ 11%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o [ 11%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o [ 11%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time 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-I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/handle_graph.cpp [ 17%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o [ 17%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o [ 20%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_acyclic.cpp gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+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 [ 85%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/split_strands.cpp cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h [ 88%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/chop.cpp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv 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inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp [ 91%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp 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 rm -f lib/libstructures.a mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o cp inc/sonLibString.h ../lib/sonLibString.h.tmp ar: creating lib/libstructures.a mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h [ 94%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/extend.cpp cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h 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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -I inc -I ../lib/ -c impl/*.c -- Performing Test HAVE_CXA_DEMANGLE gcc -o ssw_test ssw.o main.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -pipe -O3 -I. -lm -lz gcc -o example_c ssw.o example.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -pipe -O3 -I. -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:102 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio g++ -o example_cpp example.cpp ssw.o ssw_cpp.o -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -pipe -O3 -I. -lm -lz cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ src/gssw.c: In function ‘gssw_sw_software_byte’: src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 277 | memcpy(scratch, to_unswizzle, size); | ^ In function ‘unswizzle_byte’, inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Looking for C++ include cstdio - found -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Configuring done (5.2s) -- Generating done (0.3s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' ar: creating /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 8 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_config.cpp [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bits.cpp [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/config.cpp [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_isa.cpp [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/io.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/louds_tree.cpp [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/memory_management.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_fs.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sd_vector.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sfstream.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o -MF CMakeFiles/sdsl.dir/simple_sds.cpp.o.d -o CMakeFiles/sdsl.dir/simple_sds.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/simple_sds.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/structure_tree.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint128_t.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/wt_helper.cpp src/gssw.c: In function ‘gssw_sw_software_word’: src/gssw.c:1117:5: warning: ‘__builtin_memcpy’ writing between 18446744069414584336 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 1117 | memcpy(scratch, to_unswizzle, size * sizeof(int16_t)); | ^ In function ‘unswizzle_word’, inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4975:5: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 4975 | strncpy(n->seq, seq, len); n->seq[len] = 0; | ^ src/gssw.c:4971:19: note: length computed here 4971 | int32_t len = strlen(seq); | ^~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/vector:63, from /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:8: In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = long int]’, inlined from ‘static void std::allocator_traits >::deallocate(allocator_type&, pointer, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:544:23, inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:389:19, inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:368:15, inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:738:7, inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:445:5: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: ‘void operator delete(void*, std::size_t)’ called on pointer ‘’ with nonzero offset [1, 9223372036854775800] [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = long int]’, inlined from ‘static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:509:28, inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:398:44, inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:334:26, inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const value_type&, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:571:47, inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:327:85: /usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from ‘void* operator new(std::size_t)’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 33%] Linking CXX static library libkff.a cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:765:75: note: declared here 765 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:773:68: note: declared here 773 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:774:68: note: declared here 774 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-1.59.0+ds/deps/kff-cpp-api/build' impl/sonLibConnectivity.c: In function ‘stConnectivity_addEdge’: impl/sonLibConnectivity.c:248:33: warning: pointer ‘component1’ may be used after ‘free’ [-Wuse-after-free] 248 | connectivity->mergeCallback(connectivity->mergeExtraData, component1, component2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘stConnectedComponent_destruct’, inlined from ‘stConnectivity_addEdge’ at impl/sonLibConnectivity.c:238:3: impl/sonLibConnectivity.c:608:9: note: call to ‘free’ here 608 | free(comp); | ^~~~~~~~~~ [ 33%] Built target kff ar rc /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 50%] Building CXX object benchmarks/CMakeFiles/reader_bench.dir/reader.cpp.o [ 66%] Building CXX object CMakeFiles/kff_example.dir/main.cpp.o In file included from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1358:27, inlined from ‘void sdsl::int_vector< >::resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:380:23, inlined from ‘sdsl::int_vector< >::int_vector(size_type, value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1285:11, inlined from ‘sdsl::excess::impl::impl()’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:448:9: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 448 | *word &= | ^~~~~ ranlib /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 83%] Linking CXX executable reader_bench # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 83%] Built target reader_bench cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Linking CXX executable kff_example 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-1.59.0+ds/deps/kff-cpp-api/build' [100%] Built target kff_example make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibTreap.c: In function ‘stTreap_remove’: impl/sonLibTreap.c:331:18: warning: pointer ‘rmnode’ used after ‘free’ [-Wuse-after-free] 331 | stTreap *p = rmnode->parent; | ^ impl/sonLibTreap.c:329:9: note: call to ‘free’ here 329 | free(rmnode); | ^~~~~~~~~~~~ make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 94%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 97%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 [100%] 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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/g++ -fPIC -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,--dependency-file,CMakeFiles/handlegraph_shared.dir/link.d -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/dfs.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_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.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/mutable_path_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/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Built target handlegraph_shared /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.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_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.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/mutable_path_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/chop.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-1.59.0+ds/deps/libhandlegraph/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Built target handlegraph_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 94%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 97%] Built target handlegraph_static [100%] Built target handlegraph_shared make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' Install the project... /usr/bin/cmake -P cmake_install.cmake cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.a -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_metadata.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_metadata.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_position_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/util.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/buildable_snarl_decomposition.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/trivially_serializable.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/iteratee.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_tips.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/count_walks.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/split_strands.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/eades_algorithm.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/are_equivalent.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dijkstra.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/append_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/apply_orientations.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal/dfs.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dagify.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/reverse_complement.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_shortest_paths.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/topological_sort.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/copy_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/strongly_connected_components.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/chop.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/extend.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/weakly_connected_components.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_single_stranded.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_acyclic.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/snarl_decomposition.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/types.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/named_node_back_translation.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphConfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphConfigVersion.cmake make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' rm -f /build/reproducible-path/vg-1.59.0+ds/include/vg.pb.h /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp" && export LDFLAGS="-Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && rm -rf build-vg && mkdir build-vg && cd build-vg && PKG_CONFIG_PATH=/build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig: cmake -DCMAKE_CXX_STANDARD=14 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH="/usr;/" -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make clean && VERBOSE=1 make && make install cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") Building libvgio for C++ 14 -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Could NOT find Protobuf (missing: Protobuf_DIR) No installed Protobuf has registered itself with CMake. -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.21.12") Found Protobuf using FindProtobuf.cmake -- Found Threads: TRUE Using real Threads library -- Checking for module 'htslib' -- Found htslib, version 1.20 -- Checking for module 'jansson' -- Found jansson, version 2.14 Using installed libhandlegraph -- Configuring done (1.1s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make -f CMakeFiles/test_libvgio.dir/build.make CMakeFiles/test_libvgio.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake /usr/bin/cmake -P CMakeFiles/test_libvgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 0%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 2%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto [ 5%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg 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/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/basic_stream.cpp /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_emitter.cpp [ 23%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 26%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/vg.pb.cc.o -MF CMakeFiles/vgio_static.dir/vg.pb.cc.o.d -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/vg.pb.cc /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/basic_stream.cpp [ 29%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_emitter.cpp [ 35%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o [ 35%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o.d -o 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/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/json2pb.cpp /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/hfile_cppstream.cpp /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/registry.cpp.o -MF CMakeFiles/vgio.dir/src/registry.cpp.o.d -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/registry.cpp /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/stream.cpp.o -MF CMakeFiles/vgio.dir/src/stream.cpp.o.d -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream.cpp /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream_multiplexer.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 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 [100%] Linking CXX static library libsdsl.a cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm 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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm /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/simple_sds.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 /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/reproducible-path/vg-1.59.0+ds/include/sdsl/*' rm -f '/build/reproducible-path/vg-1.59.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bits.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: 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Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/io.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/iterators.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rle_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/simple_sds.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/util.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/vectors.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libsdsl.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/reproducible-path/vg-1.59.0+ds/include'. The library files are located in '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include/ && cd deps/gcsa2 && make directories && make lib/libgcsa2.a && mv lib/libgcsa2.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwt && make clean && make && mv lib/libgbwt.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/reproducible-path/vg-1.59.0+ds/include:/build/reproducible-path/vg-1.59.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp" make && cp lib/libbdsg.a /build/reproducible-path/vg-1.59.0+ds/lib && cp -r bdsg/include/* /build/reproducible-path/vg-1.59.0+ds/include rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' mkdir -p bin mkdir -p lib rm -rf bin lib obj mkdir -p obj make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' rm -f *.o *.a build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' [ ! -e bdsg/obj ] || rm -r bdsg/obj cd tests && make clean /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dbg.o src/dbg.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gcsa.o src/gcsa.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/lcp.o src/lcp.cpp rm -f test_bwtmerge test_metadata test_queries test_support test_variants *.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_graph.o src/path_graph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' mkdir -p bin mkdir -p lib mkdir -p obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/bwtmerge.o src/bwtmerge.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwt.o src/cached_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dynamic_gbwt.o src/dynamic_gbwt.cpp [ ! -e lib ] || rm -r lib /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/fast_locate.o src/fast_locate.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwt.o src/gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata.o src/metadata.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/test.o src/test.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/variants.o src/variants.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_gbwt.o src/build_gbwt.cpp [ ! -e bin ] || rm -r bin make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_ri.o src/build_ri.cpp mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/merge_gbwt.o src/merge_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/benchmark.o src/benchmark.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata_tool.o src/metadata_tool.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/mapped_structs.cpp -o bdsg/obj/mapped_structs.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/reference_path_overlay.cpp -o bdsg/obj/reference_path_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/packed_reference_path_overlay.cpp -o bdsg/obj/packed_reference_path_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/path_subgraph_overlay.cpp -o bdsg/obj/path_subgraph_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/subgraph_overlay.cpp -o bdsg/obj/subgraph_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o mv ../bin/sonLibTests.tmp ../bin/sonLibTests make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sonLib' . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/reproducible-path/vg-1.59.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/reproducible-path/vg-1.59.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/reproducible-path/vg-1.59.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c ar rc 3EdgeConnected.a *.o 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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I .//../sonLib/lib/ -c impl/*.c gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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 [ 97%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /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-1.59.0+ds/deps/libvgio/build-vg' [ 97%] Built target vgio_static [100%] 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 -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wl,--dependency-file,CMakeFiles/vgio.dir/link.d -Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib -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 /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [100%] Built target vgio make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 0%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 50%] Built target vgio make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [100%] Built target vgio_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' Install the project... /usr/bin/cmake -P cmake_install.cmake ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libvgio.so rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libvgio.a -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/vg -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/loader.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/json2pb.h -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/registry.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/edit.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' ar rcs lib/libgbwt.a obj/algorithms.o obj/bwtmerge.o obj/cached_gbwt.o obj/dynamic_gbwt.o obj/fast_locate.o obj/files.o obj/gbwt.o obj/internal.o obj/metadata.o obj/support.o obj/test.o obj/utils.o obj/variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_gbwt obj/build_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_ri obj/build_ri.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/merge_gbwt obj/merge_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/benchmark obj/benchmark.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/metadata_tool obj/metadata_tool.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/remove_seq obj/remove_seq.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 rm obj/build_ri.o obj/metadata_tool.o obj/benchmark.o obj/merge_gbwt.o obj/remove_seq.o obj/build_gbwt.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv lib/libgbwtgraph.a /build/reproducible-path/vg-1.59.0+ds/lib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' rm -rf bin lib obj rm -f *.o *.a gfa2gbwt cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' rm -f test_utils test_gbwtgraph test_cached_gbwtgraph test_gfa test_gbz test_minimizer test_index test_algorithms test_path_cover *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' mkdir -p bin mkdir -p lib mkdir -p obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwtgraph.o src/cached_gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwtgraph.o src/gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz.o src/gbz.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa.o src/gfa.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/minimizer.o src/minimizer.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_cover.o src/path_cover.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa2gbwt.o src/gfa2gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz_stats.o src/gbz_stats.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/kmer_freq.o src/kmer_freq.cpp ar rcs lib/libgcsa2.a obj/algorithms.o obj/dbg.o obj/files.o obj/gcsa.o obj/internal.o obj/lcp.o obj/path_graph.o obj/support.o obj/utils.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' 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/mapped_structs.o bdsg/obj/packed_graph.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/reference_path_overlay.o bdsg/obj/packed_reference_path_overlay.o bdsg/obj/path_subgraph_overlay.o bdsg/obj/subgraph_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/snarl_distance_index.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a ar rcs lib/libgbwtgraph.a obj/algorithms.o obj/cached_gbwtgraph.o obj/gbwtgraph.o obj/gbz.o obj/gfa.o obj/internal.o obj/minimizer.o obj/path_cover.o obj/utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/gfa2gbwt obj/gfa2gbwt.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/gbz_stats obj/gbz_stats.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/kmer_freq obj/kmer_freq.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 rm obj/kmer_freq.o obj/gbz_stats.o obj/gfa2gbwt.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/back_translating_alignment_emitter.o src/back_translating_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/clip.o src/clip.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/contracting_graph.o src/contracting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/explainer.o src/explainer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/flat_file_back_translation.o src/flat_file_back_translation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/gbwt_extender.o src/gbwt_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/gbwtgraph_helper.o src/gbwtgraph_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/gcsa_helper.o src/gcsa_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/job_schedule.o src/job_schedule.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/kff.o src/kff.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/kmp.o src/kmp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/mem_accelerator.o src/mem_accelerator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/minimizer_mapper_from_chains.o src/minimizer_mapper_from_chains.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/recombinator.o src/recombinator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/snarl_distance_index.o src/snarl_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/snarl_seed_clusterer.o src/snarl_seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/sparse_union_find.o src/sparse_union_find.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subpath_overlay.o src/subpath_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/traversal_clusters.o src/traversal_clusters.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/zstdutil.o src/zstdutil.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/back_translate.o src/algorithms/back_translate.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/chain_items.o src/algorithms/chain_items.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/component.o src/algorithms/component.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/find_gbwt.o src/algorithms/find_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/find_gbwtgraph.o src/algorithms/find_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/find_translation.o src/algorithms/find_translation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/intersect_path_offsets.o src/algorithms/intersect_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/locally_expand_graph.o src/algorithms/locally_expand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/min_cut_graph.o src/algorithms/min_cut_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/pad_band.o src/algorithms/pad_band.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/prune_to_connecting_graph.o src/algorithms/prune_to_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_params_json.o src/io/register_loader_params_json.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbz.o src/io/register_loader_saver_gbz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbzgraph.o src/io/register_loader_saver_gbzgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gfa.o src/io/register_loader_saver_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/back_translate.o src/unittest/back_translate.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/chain_items.o src/unittest/chain_items.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/component_paths.o src/unittest/component_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/gbwt_extender.o src/unittest/gbwt_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/index_helpers.o src/unittest/index_helpers.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/kff.o src/unittest/kff.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/kmp.o src/unittest/kmp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/locally_expand_graph.o src/unittest/locally_expand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/mem_accelerator.o src/unittest/mem_accelerator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/min_cut_graph.o src/unittest/min_cut_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/protobuf.o src/unittest/protobuf.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/snarl_distance_index.o src/unittest/snarl_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/snarl_seed_clusterer.o src/unittest/snarl_seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/transcriptome.o src/unittest/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/chain_main.o src/subcommand/chain_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/clip_main.o src/subcommand/clip_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/haplotypes_main.o src/subcommand/haplotypes_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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:147:31: required from here 147 | gs.stream_sort(gam_in, cout, index.get()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/any.h:38, from /usr/include/google/protobuf/generated_message_util.h:52, from /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4: /usr/include/google/protobuf/message_lite.h:381:7: note: declared here 381 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/options.o src/subcommand/options.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/config/allocator_config_jemalloc.o src/config/allocator_config_jemalloc.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/back_translating_alignment_emitter.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/clip.o obj/cluster.o obj/constructor.o obj/contracting_graph.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/explainer.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flat_file_back_translation.o obj/flow_sort.o obj/funnel.o obj/gbwt_extender.o obj/gbwt_helper.o obj/gbwtgraph_helper.o obj/gcsa_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/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/job_schedule.o obj/kff.o obj/kmer.o obj/kmp.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/mem_accelerator.o obj/memoizing_graph.o obj/memusage.o obj/minimizer_mapper.o obj/minimizer_mapper_from_chains.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/recombinator.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarl_distance_index.o obj/snarl_seed_clusterer.o obj/snarls.o obj/source_sink_overlay.o obj/sparse_union_find.o obj/splicing.o obj/split_strand_graph.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/subpath_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_clusters.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/zstdutil.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/back_translate.o obj/algorithms/chain_items.o obj/algorithms/component.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/find_gbwt.o obj/algorithms/find_gbwtgraph.o obj/algorithms/find_translation.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/intersect_path_offsets.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/locally_expand_graph.o obj/algorithms/merge.o obj/algorithms/min_cut_graph.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/pad_band.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/prune_to_connecting_graph.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/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_params_json.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_gbz.o obj/io/register_loader_saver_gbzgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_gfa.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_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++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -o test/build_graph test/build_graph.cpp -Wl,-z,relro -Wl,-z,now lib/libvg.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph -lfastahack -lhts -ltabixpp -lcairo -lm -ldl -lz -lz -lm -lz -lfontconfig -lz -lz -lm -lz -lbrotlicommon -lexpat -lm -lfreetype -lz -lbz2 -lpng16 -lz -lm -lz -lbrotlidec -lbrotlicommon -lX11 -lpthread -lxcb -lXau -lXext -lpthread -lxcb -lXau -lXrender -lX11 -lpthread -lxcb -lXau -lX11 -lpthread -lXau -lxcb -lXau -lxcb-render -lxcb -lXau -lxcb-shm -lxcb -lXau -lXdmcp -lpixman-1 -lm -pthread -lzstd -pthread -rdynamic -ldw -lelf -latomic "-lboost_program_options""" -ldl -llzma -lzstd /usr/lib/x86_64-linux-gnu/libjemalloc.a -Wl,-Bstatic -lvgio -lhts -ldeflate -lz -llzma -lprotobuf -lz -ljansson -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -o bin/vg-avx obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/back_translate.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/chain_items.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/component_paths.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/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gbwt_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_helpers.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/kff.o obj/unittest/kmp.o obj/unittest/locally_expand_graph.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/mem_accelerator.o obj/unittest/min_cut_graph.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/protobuf.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/sequence_complexity.o obj/unittest/snarl_distance_index.o obj/unittest/snarl_seed_clusterer.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.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/transcriptome.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/chain_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/clip_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/haplotypes_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/options.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_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/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 obj/config/allocator_config_jemalloc.o -Wl,-z,relro -Wl,-z,now lib/libvg.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph -lfastahack -lhts -ltabixpp -lcairo -lm -ldl -lz -lz -lm -lz -lfontconfig -lz -lz -lm -lz -lbrotlicommon -lexpat -lm -lfreetype -lz -lbz2 -lpng16 -lz -lm -lz -lbrotlidec -lbrotlicommon -lX11 -lpthread -lxcb -lXau -lXext -lpthread -lxcb -lXau -lXrender -lX11 -lpthread -lxcb -lXau -lX11 -lpthread -lXau -lxcb -lXau -lxcb-render -lxcb -lXau -lxcb-shm -lxcb -lXau -lXdmcp -lpixman-1 -lm -pthread -lzstd -pthread -rdynamic -ldw -lelf -latomic "-lboost_program_options""" -ldl -llzma -lzstd /usr/lib/x86_64-linux-gnu/libjemalloc.a -Wl,-Bstatic -lvgio -lhts -ldeflate -lz -llzma -lprotobuf -lz -ljansson -Wl,-Bdynamic -lpthread -lm make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC CXXFLAGS are -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp LDFLAGS are -Wl,-z,relro -Wl,-z,now rm -f -r bin/unittest rm -f -r lib rm -f -r obj/unittest/support rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/pic/io rm -f -r obj/io rm -f -r obj/pic/algorithms rm -f -r obj/algorithms rm -f -r obj/config rm -f -r obj/pic rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' rm -rf bin lib obj rm -f *.o *.a build_gcsa convert_graph gcsa_format try_extend cd benchmark && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2/benchmark' rm -f count_kmers query_gcsa csa_builder csa_query *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2/benchmark' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' rm -rf bin lib obj rm -f *.o *.a build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' rm -f test_bwtmerge test_metadata test_queries test_support test_variants *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' rm -rf bin lib obj rm -f *.o *.a gfa2gbwt cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' rm -f test_utils test_gbwtgraph test_cached_gbwtgraph test_gfa test_gbz test_minimizer test_index test_algorithms test_path_cover *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' cd ./deps && cd kff-cpp-api && rm -Rf build cd ./deps && cd gssw && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' cd ./deps && cd ssw && cd src && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' rm -f ssw.o ssw_cpp.o ssw_test libssw.so example_c example_cpp libsswjni.so ssw.jar ssw/Aligner.class ssw/Alignment.class ssw/Example.class *~ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/progress_bar' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/nonexistent/first-build/lib' and '/nonexistent/first-build/include' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake "--color=" make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -P /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vectors.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bits.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_g.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_comma.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/config.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_bwt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_config.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_isa.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_wt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_fully.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_iterators.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sct3.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/dac_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/enc_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/fast_cache.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/hyb_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/io.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/iterators.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_byte.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_dac.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_wt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/louds_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/memory_management.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/qsufsort.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_fs.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/raster_img.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rle_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sd_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_scan.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sfstream.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/simple_sds.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/structure_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_trees.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint128_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint256_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uintx_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/util.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/vectors.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/vlc_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wm_int.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_ap.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_blcd.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_gmr.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_huff.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_hutu.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_int.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_pc.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/lib/libsdsl.a" - not found -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vector_il.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vectors.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bits.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_g.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_gg.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_comma.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_delta.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_gamma.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_fibonacci.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/config.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_bwt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_config.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_isa.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa_se.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_alphabet_strategy.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_bitcompressed.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sampling_strategy.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_wt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_fully.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_iterators.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sct3.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/dac_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/enc_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/fast_cache.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/hyb_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_buffer.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_io_wrappers.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_mapper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/inv_perm_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/io.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/iterators.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_bitcompressed.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_byte.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_dac.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree2.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_vlc.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_wt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/louds_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/memory_management.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/nn_dict_dynamic.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/qsufsort.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_filebuf.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_fs.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_scan.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v5.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/raster_img.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rle_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sct.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support_sparse_table.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector_15.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sd_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sdsl_concepts.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_mcl.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_scan.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sfstream.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/simple_sds.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_int_stack.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_multi_stack_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_stack_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/structure_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_arrays.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_trees.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint128_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint256_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uintx_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/util.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/vectors.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/vlc_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wavelet_trees.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wm_int.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_ap.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_blcd.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_gmr.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_huff.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_hutu.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_int.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_pc.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_rlmn.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd sha1 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' rm -f /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && rm -Rf build CMakeCache.txt CMakeFiles cd ./deps && cd libvgio && rm -Rf build CMakeCache.txt CMakeFiles # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' make -j42 "INSTALL=install --strip-program=true" SFX=-sse4.1 all test/build_graph bin/shuf make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC CXXFLAGS are -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp LDFLAGS are -Wl,-z,relro -Wl,-z,now . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp" ./install.sh /build/reproducible-path/vg-1.59.0+ds . ./source_me.sh && cd deps/ssw/src && make && ar rs /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a ssw.o ssw_cpp.o && cp ssw_cpp.h ssw.h /build/reproducible-path/vg-1.59.0+ds/include . ./source_me.sh && cd deps/libhandlegraph && rm -Rf build CMakeCache.txt CMakeFiles && mkdir build && cd build && CXXFLAGS="-std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make && make install . ./source_me.sh && cd deps/kff-cpp-api && rm -Rf build && mkdir build && cd build && cmake .. && make && cp kff_io.hpp /build/reproducible-path/vg-1.59.0+ds/include && mv libkff.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && cd deps/gssw && make && cp lib/libgssw.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp src/gssw.h /build/reproducible-path/vg-1.59.0+ds/include/ . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/reproducible-path/vg-1.59.0+ds/include" make libs && cp lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/lib/ && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS && cp src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp -r src/include/structures /build/reproducible-path/vg-1.59.0+ds/include/ rm -f lib/cleaned_old_protobuf* make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' gcc -c -o ssw.o ssw.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -pipe -O3 -I. g++ -c -o ssw_cpp.o ssw_cpp.cpp -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -pipe -O3 -I. gcc -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c Library will be installed in '/build/reproducible-path/vg-1.59.0+ds' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd externalTools && make all make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. if [ ! -d obj ]; then mkdir -p obj; fi rm -f /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/* rm -Rf include/google/protobuf deps/protobuf if [ ! -d lib ]; then mkdir -p lib; fi make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make all cd quicktree_1.1 && make all CC="gcc -std=c99" touch lib/cleaned_old_protobuf_v003 find bin obj lib -type f -delete make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj; fi gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c if [ ! -d obj ]; then mkdir -p obj; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c if [ ! -d lib ]; then mkdir -p lib; fi . ./source_me.sh && g++ -I -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/progress_bar.o deps/progress_bar/progress_bar.cpp if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test; fi g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/union_find.cpp -o obj/union_find.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps; fi make[2]: 'bin/shuf' is up to date. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_graph_print’: src/gssw.c:1947:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1947 | fprintf(stdout, "GRAPH // node %llu %u %s\n", n->id, n->len, n->seq); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c:1951:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1951 | fprintf(stdout, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c:1951:56: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1951 | fprintf(stdout, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c: In function ‘gssw_graph_print_stderr’: src/gssw.c:1963:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1963 | fprintf(stderr, "GRAPH // node %llu %u %s\n", n->id, n->len, n->seq); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c:1967:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1967 | fprintf(stderr, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c:1967:56: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1967 | fprintf(stderr, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c: In function ‘gssw_graph_print_score_matrices’: src/gssw.c:1978:31: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1978 | fprintf(out, "node %llu\n", n->id); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c: In function ‘gssw_print_graph_cigar’: src/gssw.c:3623:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 3623 | fprintf(out, "%llu[", nc->node->id); | ~~~^ ~~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c: In function ‘gssw_create_seed_byte’: -- The C compiler identification is GNU 14.2.0 src/gssw.c:5095:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5095 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); | ~~~^ ~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c: In function ‘gssw_create_seed_word’: src/gssw.c:5130:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5130 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); | ~~~^ ~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ ar rc cuTest.a *.o -- The CXX compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info ranlib cuTest.a -- The C compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' -- Detecting C compiler ABI info - done -- Detecting C compiler ABI info - done -- Detecting CXX compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features -- Detecting C compile features - done -- Detecting C compile features - done gcc -o ssw_test ssw.o main.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -pipe -O3 -I. -lm -lz gcc -o example_c ssw.o example.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -pipe -O3 -I. -lm -lz -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info -- Detecting C compiler ABI info gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm g++ -o example_cpp example.cpp ssw.o ssw_cpp.o -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -pipe -O3 -I. -lm -lz cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp cp inc/bioioC.h ../lib/bioioC.h.tmp cp inc/commonC.h ../lib/commonC.h.tmp cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp cp inc/hashTableC.h ../lib/hashTableC.h.tmp cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h mv ../lib/bioioC.h.tmp ../lib/bioioC.h mv ../lib/commonC.h.tmp ../lib/commonC.h mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp cp inc/sonLib.h ../lib/sonLib.h.tmp cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h 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 cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h 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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o -- Detecting C compiler ABI info - done ar: creating lib/libstructures.a -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' -- Detecting CXX compiler ABI info - done -- Detecting CXX compiler ABI info - done -- Compiler is recent enough to support C++14. -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG src/gssw.c: In function ‘gssw_sw_software_byte’: src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 277 | memcpy(scratch, to_unswizzle, size); | ^ In function ‘unswizzle_byte’, inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done libhandlegraph is root project or external_project -- Configuring done (2.1s) -- Generating done (0.0s) make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' ar: creating /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 -- Configuring done (2.4s) /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/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[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" -- Generating done (0.0s) make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 5%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o [ 5%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o [ 8%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o [ 14%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o [ 17%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o [ 17%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ [ 20%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o 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)) { | ^ [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o 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)) { | ^ [ 28%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -MF 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-ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dijkstra.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_acyclic.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/split_strands.cpp [ 91%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/reverse_complement.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/chop.cpp [ 94%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/extend.cpp -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 16%] Building CXX object CMakeFiles/kff.dir/kff_io.cpp.o -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS src/gssw.c: In function ‘gssw_sw_software_word’: src/gssw.c:1117:5: warning: ‘__builtin_memcpy’ writing between 18446744069414584336 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 1117 | memcpy(scratch, to_unswizzle, size * sizeof(int16_t)); | ^ In function ‘unswizzle_word’, inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Performing Test HAVE_CXA_DEMANGLE src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4975:5: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 4975 | strncpy(n->seq, seq, len); n->seq[len] = 0; | ^ src/gssw.c:4971:19: note: length computed here 4971 | int32_t len = strlen(seq); | ^~~~~~~~~~~ -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:102 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio 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 /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/vector:63, from /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:8: In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = long int]’, inlined from ‘static void std::allocator_traits >::deallocate(allocator_type&, pointer, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:544:23, inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:389:19, inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:368:15, inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:738:7, inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:445:5: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: ‘void operator delete(void*, std::size_t)’ called on pointer ‘’ with nonzero offset [1, 9223372036854775800] [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = long int]’, inlined from ‘static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:509:28, inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:398:44, inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:334:26, inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const value_type&, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:571:47, inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:327:85: /usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from ‘void* operator new(std::size_t)’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -- Looking for C++ include cstdio - found -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Configuring done (6.3s) cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Generating done (0.5s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 8 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_config.cpp [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bits.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/config.cpp [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_isa.cpp [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa.cpp [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/io.cpp [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/louds_tree.cpp [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/memory_management.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_fs.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sd_vector.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sfstream.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o -MF CMakeFiles/sdsl.dir/simple_sds.cpp.o.d -o CMakeFiles/sdsl.dir/simple_sds.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/simple_sds.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/structure_tree.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint128_t.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/wt_helper.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 33%] Linking CXX static library libkff.a ar rc /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/reproducible-path/vg-1.59.0+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 impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:765:75: note: declared here 765 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:773:68: note: declared here 773 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:774:68: note: declared here 774 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ranlib /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 33%] Built target kff make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 50%] Building CXX object benchmarks/CMakeFiles/reader_bench.dir/reader.cpp.o [ 66%] Building CXX object CMakeFiles/kff_example.dir/main.cpp.o impl/sonLibConnectivity.c: In function ‘stConnectivity_addEdge’: impl/sonLibConnectivity.c:248:33: warning: pointer ‘component1’ may be used after ‘free’ [-Wuse-after-free] 248 | connectivity->mergeCallback(connectivity->mergeExtraData, component1, component2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘stConnectedComponent_destruct’, inlined from ‘stConnectivity_addEdge’ at impl/sonLibConnectivity.c:238:3: impl/sonLibConnectivity.c:608:9: note: call to ‘free’ here 608 | free(comp); | ^~~~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 83%] Linking CXX executable reader_bench In file included from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1358:27, inlined from ‘void sdsl::int_vector< >::resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:380:23, inlined from ‘sdsl::int_vector< >::int_vector(size_type, value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1285:11, inlined from ‘sdsl::excess::impl::impl()’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:448:9: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 448 | *word &= | ^~~~~ 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-1.59.0+ds/deps/kff-cpp-api/build' [ 83%] Built target reader_bench cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Linking CXX executable kff_example make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [100%] Built target kff_example make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 94%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 97%] Linking CXX shared library libhandlegraph.so [100%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/g++ -fPIC -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,--dependency-file,CMakeFiles/handlegraph_shared.dir/link.d -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/dfs.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_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.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/mutable_path_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/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Built target handlegraph_shared impl/sonLibTreap.c: In function ‘stTreap_remove’: impl/sonLibTreap.c:331:18: warning: pointer ‘rmnode’ used after ‘free’ [-Wuse-after-free] 331 | stTreap *p = rmnode->parent; | ^ impl/sonLibTreap.c:329:9: note: call to ‘free’ here 329 | free(rmnode); | ^~~~~~~~~~~~ /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.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_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.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/mutable_path_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/chop.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-1.59.0+ds/deps/libhandlegraph/build' [100%] Built target handlegraph_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 94%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 97%] Built target handlegraph_static make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Built target handlegraph_shared make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.a -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_metadata.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_metadata.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_position_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/util.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/buildable_snarl_decomposition.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/trivially_serializable.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/iteratee.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_tips.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/count_walks.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/split_strands.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/eades_algorithm.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/are_equivalent.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dijkstra.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/append_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/apply_orientations.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal/dfs.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dagify.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/reverse_complement.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_shortest_paths.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/topological_sort.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/copy_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/strongly_connected_components.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/chop.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/extend.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/weakly_connected_components.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_single_stranded.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_acyclic.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/snarl_decomposition.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/types.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/named_node_back_translation.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphConfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphConfigVersion.cmake make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' rm -f /build/reproducible-path/vg-1.59.0+ds/include/vg.pb.h /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp" && export LDFLAGS="-Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && rm -rf build-vg && mkdir build-vg && cd build-vg && PKG_CONFIG_PATH=/build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig: cmake -DCMAKE_CXX_STANDARD=14 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH="/usr;/" -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make clean && VERBOSE=1 make && make install cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done 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 -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") Building libvgio for C++ 14 -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Could NOT find Protobuf (missing: Protobuf_DIR) No installed Protobuf has registered itself with CMake. [100%] Linking CXX static library libsdsl.a cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.21.12") Found Protobuf using FindProtobuf.cmake -- Found Threads: TRUE Using real Threads library -- Checking for module 'htslib' -- Found htslib, version 1.20 -- Checking for module 'jansson' -- Found jansson, version 2.14 Using installed libhandlegraph -- Configuring done (1.2s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make -f CMakeFiles/test_libvgio.dir/build.make CMakeFiles/test_libvgio.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/test_libvgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 0%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 2%] Running cpp protocol buffer compiler on deps/vg.proto [ 5%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 11%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o [ 8%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o [ 17%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o [ 17%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o [ 20%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/hfile_cppstream.cpp [ 23%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o [ 26%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/basic_stream.cpp /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/simple_sds.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 /usr/bin/ranlib libsdsl.a /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/edit.cpp.o -MF CMakeFiles/vgio.dir/src/edit.cpp.o.d -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/edit.cpp /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_emitter.cpp [ 29%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_iterator.cpp [ 35%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o [ 35%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/registry.cpp.o -MF CMakeFiles/vgio.dir/src/registry.cpp.o.d -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/registry.cpp [ 38%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/vg.pb.cc.o -MF CMakeFiles/vgio.dir/vg.pb.cc.o.d -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/vg.pb.cc [ 44%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o [ 44%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 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47%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/json2pb.cpp [ 50%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/stream.cpp.o -MF CMakeFiles/vgio.dir/src/stream.cpp.o.d -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream.cpp /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream_multiplexer.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg 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-I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 79%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o [ 82%] Building CXX object 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/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/hfile_cppstream.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg 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/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream_multiplexer.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio_static.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/vpkg.cpp [100%] Built target sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/reproducible-path/vg-1.59.0+ds/include/sdsl/*' rm -f '/build/reproducible-path/vg-1.59.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bits.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/config.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/io.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/iterators.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rle_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/simple_sds.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/util.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/vectors.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libsdsl.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/reproducible-path/vg-1.59.0+ds/include'. The library files are located in '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include/ && cd deps/gcsa2 && make directories && make lib/libgcsa2.a && mv lib/libgcsa2.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwt && make clean && make && mv lib/libgbwt.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/reproducible-path/vg-1.59.0+ds/include:/build/reproducible-path/vg-1.59.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp" make && cp lib/libbdsg.a /build/reproducible-path/vg-1.59.0+ds/lib && cp -r bdsg/include/* /build/reproducible-path/vg-1.59.0+ds/include rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' mkdir -p bin mkdir -p lib rm -rf bin lib obj mkdir -p obj rm -f *.o *.a build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' [ ! -e bdsg/obj ] || rm -r bdsg/obj make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dbg.o src/dbg.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp rm -f test_bwtmerge test_metadata test_queries test_support test_variants *.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gcsa.o src/gcsa.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/lcp.o src/lcp.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_graph.o src/path_graph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' [ ! -e lib ] || rm -r lib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' mkdir -p bin mkdir -p lib mkdir -p obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp [ ! -e bin ] || rm -r bin make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/bwtmerge.o src/bwtmerge.cpp make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwt.o src/cached_gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dynamic_gbwt.o src/dynamic_gbwt.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/fast_locate.o src/fast_locate.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwt.o src/gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata.o src/metadata.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp 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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/mapped_structs.cpp -o bdsg/obj/mapped_structs.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/test.o src/test.cpp mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/variants.o src/variants.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_gbwt.o src/build_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_ri.o src/build_ri.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/merge_gbwt.o src/merge_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/benchmark.o src/benchmark.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/reference_path_overlay.cpp -o bdsg/obj/reference_path_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata_tool.o src/metadata_tool.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/packed_reference_path_overlay.cpp -o bdsg/obj/packed_reference_path_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/path_subgraph_overlay.cpp -o bdsg/obj/path_subgraph_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/subgraph_overlay.cpp -o bdsg/obj/subgraph_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o mv ../bin/sonLibTests.tmp ../bin/sonLibTests make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sonLib' . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/reproducible-path/vg-1.59.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/reproducible-path/vg-1.59.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/reproducible-path/vg-1.59.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c [ 97%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 ar rc 3EdgeConnected.a *.o 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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm [100%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I .//../sonLib/lib/ -c impl/*.c gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wl,--dependency-file,CMakeFiles/vgio.dir/link.d -Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib -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 /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [100%] Built target vgio /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-1.59.0+ds/deps/libvgio/build-vg' [100%] Built target vgio_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 0%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 50%] Built target vgio_static [100%] Built target vgio make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libvgio.so -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libvgio.a -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/vg -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/loader.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/json2pb.h -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/registry.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/edit.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' ar rcs lib/libgbwt.a obj/algorithms.o obj/bwtmerge.o obj/cached_gbwt.o obj/dynamic_gbwt.o obj/fast_locate.o obj/files.o obj/gbwt.o obj/internal.o obj/metadata.o obj/support.o obj/test.o obj/utils.o obj/variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_gbwt obj/build_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_ri obj/build_ri.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/merge_gbwt obj/merge_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/benchmark obj/benchmark.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/metadata_tool obj/metadata_tool.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/remove_seq obj/remove_seq.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 rm obj/build_ri.o obj/metadata_tool.o obj/benchmark.o obj/merge_gbwt.o obj/remove_seq.o obj/build_gbwt.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv lib/libgbwtgraph.a /build/reproducible-path/vg-1.59.0+ds/lib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' rm -rf bin lib obj rm -f *.o *.a gfa2gbwt cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' rm -f test_utils test_gbwtgraph test_cached_gbwtgraph test_gfa test_gbz test_minimizer test_index test_algorithms test_path_cover *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' mkdir -p bin mkdir -p lib mkdir -p obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwtgraph.o src/cached_gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwtgraph.o src/gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz.o src/gbz.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa.o src/gfa.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/minimizer.o src/minimizer.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_cover.o src/path_cover.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa2gbwt.o src/gfa2gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz_stats.o src/gbz_stats.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/kmer_freq.o src/kmer_freq.cpp 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/mapped_structs.o bdsg/obj/packed_graph.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/reference_path_overlay.o bdsg/obj/packed_reference_path_overlay.o bdsg/obj/path_subgraph_overlay.o bdsg/obj/subgraph_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/snarl_distance_index.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a ar rcs lib/libgcsa2.a obj/algorithms.o obj/dbg.o obj/files.o obj/gcsa.o obj/internal.o obj/lcp.o obj/path_graph.o obj/support.o obj/utils.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a ar rcs lib/libgbwtgraph.a obj/algorithms.o obj/cached_gbwtgraph.o obj/gbwtgraph.o obj/gbz.o obj/gfa.o obj/internal.o obj/minimizer.o obj/path_cover.o obj/utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/gfa2gbwt obj/gfa2gbwt.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/gbz_stats obj/gbz_stats.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/kmer_freq obj/kmer_freq.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 rm obj/kmer_freq.o obj/gbz_stats.o obj/gfa2gbwt.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/back_translating_alignment_emitter.o src/back_translating_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/clip.o src/clip.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/contracting_graph.o src/contracting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/explainer.o src/explainer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/flat_file_back_translation.o src/flat_file_back_translation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/gbwt_extender.o src/gbwt_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/gbwtgraph_helper.o src/gbwtgraph_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/gcsa_helper.o src/gcsa_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/job_schedule.o src/job_schedule.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/kff.o src/kff.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/kmp.o src/kmp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/mem_accelerator.o src/mem_accelerator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/minimizer_mapper_from_chains.o src/minimizer_mapper_from_chains.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/recombinator.o src/recombinator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/snarl_distance_index.o src/snarl_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/snarl_seed_clusterer.o src/snarl_seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/sparse_union_find.o src/sparse_union_find.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subpath_overlay.o src/subpath_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/traversal_clusters.o src/traversal_clusters.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/zstdutil.o src/zstdutil.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/back_translate.o src/algorithms/back_translate.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/chain_items.o src/algorithms/chain_items.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/component.o src/algorithms/component.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/find_gbwt.o src/algorithms/find_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/find_gbwtgraph.o src/algorithms/find_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/find_translation.o src/algorithms/find_translation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/intersect_path_offsets.o src/algorithms/intersect_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/locally_expand_graph.o src/algorithms/locally_expand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/min_cut_graph.o src/algorithms/min_cut_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/pad_band.o src/algorithms/pad_band.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/prune_to_connecting_graph.o src/algorithms/prune_to_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_params_json.o src/io/register_loader_params_json.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbz.o src/io/register_loader_saver_gbz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbzgraph.o src/io/register_loader_saver_gbzgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gfa.o src/io/register_loader_saver_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/back_translate.o src/unittest/back_translate.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/chain_items.o src/unittest/chain_items.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/component_paths.o src/unittest/component_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/gbwt_extender.o src/unittest/gbwt_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/index_helpers.o src/unittest/index_helpers.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/kff.o src/unittest/kff.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/kmp.o src/unittest/kmp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/locally_expand_graph.o src/unittest/locally_expand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/mem_accelerator.o src/unittest/mem_accelerator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/min_cut_graph.o src/unittest/min_cut_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/protobuf.o src/unittest/protobuf.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/snarl_distance_index.o src/unittest/snarl_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/snarl_seed_clusterer.o src/unittest/snarl_seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/transcriptome.o src/unittest/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/chain_main.o src/subcommand/chain_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/clip_main.o src/subcommand/clip_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/haplotypes_main.o src/subcommand/haplotypes_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_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:147:31: required from here 147 | gs.stream_sort(gam_in, cout, index.get()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/any.h:38, from /usr/include/google/protobuf/generated_message_util.h:52, from /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4: /usr/include/google/protobuf/message_lite.h:381:7: note: declared here 381 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/options.o src/subcommand/options.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/config/allocator_config_jemalloc.o src/config/allocator_config_jemalloc.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/back_translating_alignment_emitter.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/clip.o obj/cluster.o obj/constructor.o obj/contracting_graph.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/explainer.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flat_file_back_translation.o obj/flow_sort.o obj/funnel.o obj/gbwt_extender.o obj/gbwt_helper.o obj/gbwtgraph_helper.o obj/gcsa_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/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/job_schedule.o obj/kff.o obj/kmer.o obj/kmp.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/mem_accelerator.o obj/memoizing_graph.o obj/memusage.o obj/minimizer_mapper.o obj/minimizer_mapper_from_chains.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/recombinator.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarl_distance_index.o obj/snarl_seed_clusterer.o obj/snarls.o obj/source_sink_overlay.o obj/sparse_union_find.o obj/splicing.o obj/split_strand_graph.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/subpath_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_clusters.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/zstdutil.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/back_translate.o obj/algorithms/chain_items.o obj/algorithms/component.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/find_gbwt.o obj/algorithms/find_gbwtgraph.o obj/algorithms/find_translation.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/intersect_path_offsets.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/locally_expand_graph.o obj/algorithms/merge.o obj/algorithms/min_cut_graph.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/pad_band.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/prune_to_connecting_graph.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/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_params_json.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_gbz.o obj/io/register_loader_saver_gbzgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_gfa.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_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++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -o test/build_graph test/build_graph.cpp -Wl,-z,relro -Wl,-z,now lib/libvg.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph -lfastahack -lhts -ltabixpp -lcairo -lm -ldl -lz -lz -lm -lz -lfontconfig -lz -lz -lm -lz -lbrotlicommon -lexpat -lm -lfreetype -lz -lbz2 -lpng16 -lz -lm -lz -lbrotlidec -lbrotlicommon -lX11 -lpthread -lxcb -lXau -lXext -lpthread -lxcb -lXau -lXrender -lX11 -lpthread -lxcb -lXau -lX11 -lpthread -lXau -lxcb -lXau -lxcb-render -lxcb -lXau -lxcb-shm -lxcb -lXau -lXdmcp -lpixman-1 -lm -pthread -lzstd -pthread -rdynamic -ldw -lelf -latomic "-lboost_program_options""" -ldl -llzma -lzstd /usr/lib/x86_64-linux-gnu/libjemalloc.a -Wl,-Bstatic -lvgio -lhts -ldeflate -lz -llzma -lprotobuf -lz -ljansson -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -o bin/vg-sse4.1 obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/back_translate.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/chain_items.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/component_paths.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/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gbwt_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_helpers.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/kff.o obj/unittest/kmp.o obj/unittest/locally_expand_graph.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/mem_accelerator.o obj/unittest/min_cut_graph.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/protobuf.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/sequence_complexity.o obj/unittest/snarl_distance_index.o obj/unittest/snarl_seed_clusterer.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.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/transcriptome.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/chain_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/clip_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/haplotypes_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/options.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_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/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 obj/config/allocator_config_jemalloc.o -Wl,-z,relro -Wl,-z,now lib/libvg.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph -lfastahack -lhts -ltabixpp -lcairo -lm -ldl -lz -lz -lm -lz -lfontconfig -lz -lz -lm -lz -lbrotlicommon -lexpat -lm -lfreetype -lz -lbz2 -lpng16 -lz -lm -lz -lbrotlidec -lbrotlicommon -lX11 -lpthread -lxcb -lXau -lXext -lpthread -lxcb -lXau -lXrender -lX11 -lpthread -lxcb -lXau -lX11 -lpthread -lXau -lxcb -lXau -lxcb-render -lxcb -lXau -lxcb-shm -lxcb -lXau -lXdmcp -lpixman-1 -lm -pthread -lzstd -pthread -rdynamic -ldw -lelf -latomic "-lboost_program_options""" -ldl -llzma -lzstd /usr/lib/x86_64-linux-gnu/libjemalloc.a -Wl,-Bstatic -lvgio -lhts -ldeflate -lz -llzma -lprotobuf -lz -ljansson -Wl,-Bdynamic -lpthread -lm make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC CXXFLAGS are -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp LDFLAGS are -Wl,-z,relro -Wl,-z,now rm -f -r bin/unittest rm -f -r lib rm -f -r obj/unittest/support rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/pic/io rm -f -r obj/io rm -f -r obj/pic/algorithms rm -f -r obj/algorithms rm -f -r obj/config rm -f -r obj/pic rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' rm -rf bin lib obj rm -f *.o *.a build_gcsa convert_graph gcsa_format try_extend cd benchmark && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2/benchmark' rm -f count_kmers query_gcsa csa_builder csa_query *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2/benchmark' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' rm -rf bin lib obj rm -f *.o *.a build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' rm -f test_bwtmerge test_metadata test_queries test_support test_variants *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' rm -rf bin lib obj rm -f *.o *.a gfa2gbwt cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' rm -f test_utils test_gbwtgraph test_cached_gbwtgraph test_gfa test_gbz test_minimizer test_index test_algorithms test_path_cover *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' cd ./deps && cd kff-cpp-api && rm -Rf build cd ./deps && cd gssw && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' cd ./deps && cd ssw && cd src && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' rm -f ssw.o ssw_cpp.o ssw_test libssw.so example_c example_cpp libsswjni.so ssw.jar ssw/Aligner.class ssw/Alignment.class ssw/Example.class *~ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/progress_bar' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/nonexistent/first-build/lib' and '/nonexistent/first-build/include' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake "--color=" make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -P /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vectors.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bits.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_g.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_comma.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/config.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_bwt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_config.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_isa.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_wt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_fully.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_iterators.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sct3.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/dac_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/enc_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/fast_cache.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/hyb_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/io.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/iterators.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_byte.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_dac.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_wt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/louds_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/memory_management.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/qsufsort.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_fs.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/raster_img.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rle_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sd_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_scan.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sfstream.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/simple_sds.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/structure_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_trees.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint128_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint256_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uintx_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/util.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/vectors.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/vlc_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wm_int.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_ap.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_blcd.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_gmr.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_huff.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_hutu.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_int.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_pc.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/lib/libsdsl.a" - not found -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vector_il.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vectors.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bits.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_g.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_gg.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_comma.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_delta.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_gamma.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_fibonacci.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/config.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_bwt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_config.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_isa.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa_se.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_alphabet_strategy.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_bitcompressed.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sampling_strategy.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_wt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_fully.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_iterators.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sct3.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/dac_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/enc_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/fast_cache.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/hyb_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_buffer.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_io_wrappers.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_mapper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/inv_perm_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/io.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/iterators.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_bitcompressed.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_byte.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_dac.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree2.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_vlc.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_wt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/louds_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/memory_management.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/nn_dict_dynamic.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/qsufsort.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_filebuf.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_fs.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_scan.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v5.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/raster_img.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rle_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sct.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support_sparse_table.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector_15.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sd_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sdsl_concepts.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_mcl.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_scan.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sfstream.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/simple_sds.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_int_stack.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_multi_stack_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_stack_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/structure_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_arrays.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_trees.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint128_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint256_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uintx_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/util.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/vectors.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/vlc_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wavelet_trees.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wm_int.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_ap.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_blcd.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_gmr.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_huff.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_hutu.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_int.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_pc.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_rlmn.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd sha1 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' rm -f /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && rm -Rf build CMakeCache.txt CMakeFiles cd ./deps && cd libvgio && rm -Rf build CMakeCache.txt CMakeFiles # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' make -j42 "INSTALL=install --strip-program=true" SFX=-ssse3 all test/build_graph bin/shuf make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC CXXFLAGS are -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp LDFLAGS are -Wl,-z,relro -Wl,-z,now . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp" ./install.sh /build/reproducible-path/vg-1.59.0+ds . ./source_me.sh && cd deps/ssw/src && make && ar rs /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a ssw.o ssw_cpp.o && cp ssw_cpp.h ssw.h /build/reproducible-path/vg-1.59.0+ds/include . ./source_me.sh && cd deps/libhandlegraph && rm -Rf build CMakeCache.txt CMakeFiles && mkdir build && cd build && CXXFLAGS="-std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make && make install . ./source_me.sh && cd deps/kff-cpp-api && rm -Rf build && mkdir build && cd build && cmake .. && make && cp kff_io.hpp /build/reproducible-path/vg-1.59.0+ds/include && mv libkff.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && cd deps/gssw && make && cp lib/libgssw.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp src/gssw.h /build/reproducible-path/vg-1.59.0+ds/include/ . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/reproducible-path/vg-1.59.0+ds/include" make libs && cp lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/lib/ && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS && cp src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp -r src/include/structures /build/reproducible-path/vg-1.59.0+ds/include/ rm -f lib/cleaned_old_protobuf* make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' gcc -c -o ssw.o ssw.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -pipe -O3 -I. g++ -c -o ssw_cpp.o ssw_cpp.cpp -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -pipe -O3 -I. gcc -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' Library will be installed in '/build/reproducible-path/vg-1.59.0+ds' rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd externalTools && make all gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. if [ ! -d obj ]; then mkdir -p obj; fi rm -Rf include/google/protobuf deps/protobuf rm -f /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/* make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make all cd quicktree_1.1 && make all CC="gcc -std=c99" if [ ! -d lib ]; then mkdir -p lib; fi touch lib/cleaned_old_protobuf_v003 find bin obj lib -type f -delete make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj; fi gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c if [ ! -d obj ]; then mkdir -p obj; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c . ./source_me.sh && g++ -I -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/progress_bar.o deps/progress_bar/progress_bar.cpp g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c if [ ! -d lib ]; then mkdir -p lib; fi gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/union_find.cpp -o obj/union_find.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o make[2]: 'bin/shuf' is up to date. if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_graph_print’: src/gssw.c:1947:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1947 | fprintf(stdout, "GRAPH // node %llu %u %s\n", n->id, n->len, n->seq); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c:1951:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1951 | fprintf(stdout, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c:1951:56: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1951 | fprintf(stdout, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c: In function ‘gssw_graph_print_stderr’: src/gssw.c:1963:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1963 | fprintf(stderr, "GRAPH // node %llu %u %s\n", n->id, n->len, n->seq); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c:1967:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1967 | fprintf(stderr, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c:1967:56: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1967 | fprintf(stderr, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c: In function ‘gssw_graph_print_score_matrices’: /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ src/gssw.c:1978:31: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1978 | fprintf(out, "node %llu\n", n->id); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c: In function ‘gssw_print_graph_cigar’: src/gssw.c:3623:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 3623 | fprintf(out, "%llu[", nc->node->id); | ~~~^ ~~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c: In function ‘gssw_create_seed_byte’: src/gssw.c:5095:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5095 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); | ~~~^ ~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c: In function ‘gssw_create_seed_word’: src/gssw.c:5130:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5130 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); | ~~~^ ~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu ar rc cuTest.a *.o -- The C compiler identification is GNU 14.2.0 -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' -- The C compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compiler ABI info - done gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp cp inc/bioioC.h ../lib/bioioC.h.tmp cp inc/commonC.h ../lib/commonC.h.tmp cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h mv ../lib/commonC.h.tmp ../lib/commonC.h mv ../lib/bioioC.h.tmp ../lib/bioioC.h mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp -- Detecting CXX compiler ABI info - done mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp cp inc/sonLib.h ../lib/sonLib.h.tmp cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h mv ../lib/sonLib.h.tmp ../lib/sonLib.h mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp cp inc/sonLibList.h ../lib/sonLibList.h.tmp cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp cp inc/sonLibString.h ../lib/sonLibString.h.tmp cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp cp inc/stGraph.h ../lib/stGraph.h.tmp cp inc/stJson.h ../lib/stJson.h.tmp cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h mv ../lib/stGraph.h.tmp ../lib/stGraph.h mv ../lib/stJson.h.tmp ../lib/stJson.h mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp -- Detecting CXX compile features - done cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h 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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Detecting C compiler ABI info -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info gcc -o ssw_test ssw.o main.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -pipe -O3 -I. -lm -lz gcc -o example_c ssw.o example.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -pipe -O3 -I. -lm -lz g++ -o example_cpp example.cpp ssw.o ssw_cpp.o -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -pipe -O3 -I. -lm -lz cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ 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 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' src/gssw.c: In function ‘gssw_sw_software_byte’: src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 277 | memcpy(scratch, to_unswizzle, size); | ^ In function ‘unswizzle_byte’, inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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)) { | ^ -- Detecting C compiler ABI info - done -- Detecting CXX compiler ABI info - done -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting CXX compile features - done -- Detecting C compile features - done libhandlegraph is root project or external_project -- Compiler is recent enough to support C++14. -- Configuring done (1.9s) -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done (1.9s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 8%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o [ 8%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o [ 8%] 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object CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o [ 28%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_metadata.cpp [ 31%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp [ 34%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o [ 37%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o [ 40%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o [ 42%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp [ 60%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o [ 62%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o [ 62%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 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directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' ar: creating /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Performing Test HAVE_CXA_DEMANGLE src/gssw.c: In function ‘gssw_sw_software_word’: src/gssw.c:1117:5: warning: ‘__builtin_memcpy’ writing between 18446744069414584336 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 1117 | memcpy(scratch, to_unswizzle, size * sizeof(int16_t)); | ^ In function ‘unswizzle_word’, inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:102 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio -- Looking for C++ include cstdio - found -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4975:5: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 4975 | strncpy(n->seq, seq, len); n->seq[len] = 0; | ^ src/gssw.c:4971:19: note: length computed here 4971 | int32_t len = strlen(seq); | ^~~~~~~~~~~ -- Configuring done (3.7s) 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 -- Generating done (0.4s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 8 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bits.cpp [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/config.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_config.cpp [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_isa.cpp [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/io.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/louds_tree.cpp [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/memory_management.cpp [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sd_vector.cpp [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_fs.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sfstream.cpp [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o -MF CMakeFiles/sdsl.dir/simple_sds.cpp.o.d -o CMakeFiles/sdsl.dir/simple_sds.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/simple_sds.cpp [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/structure_tree.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint128_t.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/wt_helper.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/vector:63, from /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:8: In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = long int]’, inlined from ‘static void std::allocator_traits >::deallocate(allocator_type&, pointer, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:544:23, inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:389:19, inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:368:15, inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:738:7, inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:445:5: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: ‘void operator delete(void*, std::size_t)’ called on pointer ‘’ with nonzero offset [1, 9223372036854775800] [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = long int]’, inlined from ‘static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:509:28, inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:398:44, inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:334:26, inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const value_type&, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:571:47, inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:327:85: /usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from ‘void* operator new(std::size_t)’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:765:75: note: declared here 765 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:773:68: note: declared here 773 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:774:68: note: declared here 774 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ar rc /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o ranlib /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' impl/sonLibConnectivity.c: In function ‘stConnectivity_addEdge’: impl/sonLibConnectivity.c:248:33: warning: pointer ‘component1’ may be used after ‘free’ [-Wuse-after-free] 248 | connectivity->mergeCallback(connectivity->mergeExtraData, component1, component2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘stConnectedComponent_destruct’, inlined from ‘stConnectivity_addEdge’ at impl/sonLibConnectivity.c:238:3: impl/sonLibConnectivity.c:608:9: note: call to ‘free’ here 608 | free(comp); | ^~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 33%] Linking CXX static library libkff.a make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 33%] Built target kff make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 66%] Building CXX object CMakeFiles/kff_example.dir/main.cpp.o [ 66%] Building CXX object benchmarks/CMakeFiles/reader_bench.dir/reader.cpp.o 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-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1358:27, inlined from ‘void sdsl::int_vector< >::resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:380:23, inlined from ‘sdsl::int_vector< >::int_vector(size_type, value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1285:11, inlined from ‘sdsl::excess::impl::impl()’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:448:9: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 448 | *word &= | ^~~~~ 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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 83%] Linking CXX executable reader_bench make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 83%] Built target reader_bench 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 [100%] Linking CXX executable kff_example 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-1.59.0+ds/deps/kff-cpp-api/build' [100%] Built target kff_example make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibTreap.c: In function ‘stTreap_remove’: impl/sonLibTreap.c:331:18: warning: pointer ‘rmnode’ used after ‘free’ [-Wuse-after-free] 331 | stTreap *p = rmnode->parent; | ^ impl/sonLibTreap.c:329:9: note: call to ‘free’ here 329 | free(rmnode); | ^~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 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 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 94%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 97%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 [100%] 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/dfs.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_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.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/mutable_path_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/chop.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-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/g++ -fPIC -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,--dependency-file,CMakeFiles/handlegraph_shared.dir/link.d -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/dfs.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_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.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/mutable_path_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/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Built target handlegraph_static [100%] Built target handlegraph_shared make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 94%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Built target handlegraph_shared [100%] Built target handlegraph_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.a -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_metadata.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_metadata.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_position_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/util.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/buildable_snarl_decomposition.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/trivially_serializable.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/iteratee.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_tips.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/count_walks.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/split_strands.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/eades_algorithm.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/are_equivalent.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dijkstra.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/append_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/apply_orientations.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal/dfs.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dagify.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/reverse_complement.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_shortest_paths.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/topological_sort.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/copy_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/strongly_connected_components.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/chop.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/extend.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/weakly_connected_components.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_single_stranded.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_acyclic.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/snarl_decomposition.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/types.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/named_node_back_translation.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphConfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphConfigVersion.cmake make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' rm -f /build/reproducible-path/vg-1.59.0+ds/include/vg.pb.h /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp" && export LDFLAGS="-Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && rm -rf build-vg && mkdir build-vg && cd build-vg && PKG_CONFIG_PATH=/build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig: cmake -DCMAKE_CXX_STANDARD=14 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH="/usr;/" -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make clean && VERBOSE=1 make && make install cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info 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 -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") Building libvgio for C++ 14 -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Could NOT find Protobuf (missing: Protobuf_DIR) No installed Protobuf has registered itself with CMake. -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.21.12") Found Protobuf using FindProtobuf.cmake -- Found Threads: TRUE Using real Threads library -- Checking for module 'htslib' -- Found htslib, version 1.20 -- Checking for module 'jansson' -- Found jansson, version 2.14 Using installed libhandlegraph -- Configuring done (0.9s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make -f CMakeFiles/test_libvgio.dir/build.make CMakeFiles/test_libvgio.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/test_libvgio.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 0%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 2%] Running cpp protocol buffer compiler on deps/vg.proto [ 5%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 11%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o [ 11%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o [ 14%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o [ 17%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o [ 20%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong 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/build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_emitter.cpp [ 82%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o [ 88%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o [ 88%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg 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CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream_multiplexer.cpp [100%] Linking CXX static library libsdsl.a cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/vg-1.59.0+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/simple_sds.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 /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/reproducible-path/vg-1.59.0+ds/include/sdsl/*' rm -f '/build/reproducible-path/vg-1.59.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bits.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/config.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/io.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/iterators.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rle_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/simple_sds.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/util.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/vectors.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libsdsl.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/reproducible-path/vg-1.59.0+ds/include'. The library files are located in '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include/ && cd deps/gcsa2 && make directories && make lib/libgcsa2.a && mv lib/libgcsa2.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwt && make clean && make && mv lib/libgbwt.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/reproducible-path/vg-1.59.0+ds/include:/build/reproducible-path/vg-1.59.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp" make && cp lib/libbdsg.a /build/reproducible-path/vg-1.59.0+ds/lib && cp -r bdsg/include/* /build/reproducible-path/vg-1.59.0+ds/include rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' mkdir -p bin mkdir -p lib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' mkdir -p obj [ ! -e bdsg/obj ] || rm -r bdsg/obj make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' rm -rf bin lib obj make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' rm -f *.o *.a build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq cd tests && make clean /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dbg.o src/dbg.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gcsa.o src/gcsa.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/lcp.o src/lcp.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_graph.o src/path_graph.cpp rm -f test_bwtmerge test_metadata test_queries test_support test_variants *.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' [ ! -e lib ] || rm -r lib mkdir -p bin mkdir -p lib mkdir -p obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/bwtmerge.o src/bwtmerge.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwt.o src/cached_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dynamic_gbwt.o src/dynamic_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/fast_locate.o src/fast_locate.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwt.o src/gbwt.cpp [ ! -e bin ] || rm -r bin make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/mapped_structs.cpp -o bdsg/obj/mapped_structs.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/reference_path_overlay.cpp -o bdsg/obj/reference_path_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_reference_path_overlay.cpp -o bdsg/obj/packed_reference_path_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/path_subgraph_overlay.cpp -o bdsg/obj/path_subgraph_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/subgraph_overlay.cpp -o bdsg/obj/subgraph_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata.o src/metadata.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/test.o src/test.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/variants.o src/variants.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_gbwt.o src/build_gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_ri.o src/build_ri.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/merge_gbwt.o src/merge_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/benchmark.o src/benchmark.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata_tool.o src/metadata_tool.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o mv ../bin/sonLibTests.tmp ../bin/sonLibTests make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sonLib' . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/reproducible-path/vg-1.59.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/reproducible-path/vg-1.59.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/reproducible-path/vg-1.59.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c ar rc 3EdgeConnected.a *.o 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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I .//../sonLib/lib/ -c impl/*.c gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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 ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' [ 97%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 [100%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wl,--dependency-file,CMakeFiles/vgio.dir/link.d -Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib -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 /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 [100%] Built target vgio /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-1.59.0+ds/deps/libvgio/build-vg' [100%] Built target vgio_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 0%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [100%] Built target vgio_static [100%] Built target vgio make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libvgio.so -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libvgio.a -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/vg -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/loader.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/json2pb.h -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/registry.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/edit.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' ar rcs lib/libgbwt.a obj/algorithms.o obj/bwtmerge.o obj/cached_gbwt.o obj/dynamic_gbwt.o obj/fast_locate.o obj/files.o obj/gbwt.o obj/internal.o obj/metadata.o obj/support.o obj/test.o obj/utils.o obj/variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_gbwt obj/build_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_ri obj/build_ri.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/merge_gbwt obj/merge_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/benchmark obj/benchmark.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/metadata_tool obj/metadata_tool.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/remove_seq obj/remove_seq.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 rm obj/build_ri.o obj/metadata_tool.o obj/benchmark.o obj/merge_gbwt.o obj/remove_seq.o obj/build_gbwt.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv lib/libgbwtgraph.a /build/reproducible-path/vg-1.59.0+ds/lib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' rm -rf bin lib obj rm -f *.o *.a gfa2gbwt cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' rm -f test_utils test_gbwtgraph test_cached_gbwtgraph test_gfa test_gbz test_minimizer test_index test_algorithms test_path_cover *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' mkdir -p bin mkdir -p lib mkdir -p obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwtgraph.o src/cached_gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwtgraph.o src/gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz.o src/gbz.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa.o src/gfa.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/minimizer.o src/minimizer.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_cover.o src/path_cover.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa2gbwt.o src/gfa2gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz_stats.o src/gbz_stats.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/kmer_freq.o src/kmer_freq.cpp 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/mapped_structs.o bdsg/obj/packed_graph.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/reference_path_overlay.o bdsg/obj/packed_reference_path_overlay.o bdsg/obj/path_subgraph_overlay.o bdsg/obj/subgraph_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/snarl_distance_index.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' ar rcs lib/libgcsa2.a obj/algorithms.o obj/dbg.o obj/files.o obj/gcsa.o obj/internal.o obj/lcp.o obj/path_graph.o obj/support.o obj/utils.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a ar rcs lib/libgbwtgraph.a obj/algorithms.o obj/cached_gbwtgraph.o obj/gbwtgraph.o obj/gbz.o obj/gfa.o obj/internal.o obj/minimizer.o obj/path_cover.o obj/utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/gfa2gbwt obj/gfa2gbwt.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/gbz_stats obj/gbz_stats.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/kmer_freq obj/kmer_freq.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 rm obj/kmer_freq.o obj/gbz_stats.o obj/gfa2gbwt.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/back_translating_alignment_emitter.o src/back_translating_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/clip.o src/clip.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/contracting_graph.o src/contracting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/explainer.o src/explainer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/flat_file_back_translation.o src/flat_file_back_translation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/gbwt_extender.o src/gbwt_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/gbwtgraph_helper.o src/gbwtgraph_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/gcsa_helper.o src/gcsa_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/job_schedule.o src/job_schedule.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/kff.o src/kff.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/kmp.o src/kmp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/mem_accelerator.o src/mem_accelerator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/minimizer_mapper_from_chains.o src/minimizer_mapper_from_chains.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/recombinator.o src/recombinator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/snarl_distance_index.o src/snarl_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/snarl_seed_clusterer.o src/snarl_seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/sparse_union_find.o src/sparse_union_find.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subpath_overlay.o src/subpath_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/traversal_clusters.o src/traversal_clusters.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/zstdutil.o src/zstdutil.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/back_translate.o src/algorithms/back_translate.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/chain_items.o src/algorithms/chain_items.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/component.o src/algorithms/component.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/find_gbwt.o src/algorithms/find_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/find_gbwtgraph.o src/algorithms/find_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/find_translation.o src/algorithms/find_translation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/intersect_path_offsets.o src/algorithms/intersect_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/locally_expand_graph.o src/algorithms/locally_expand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/min_cut_graph.o src/algorithms/min_cut_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/pad_band.o src/algorithms/pad_band.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/prune_to_connecting_graph.o src/algorithms/prune_to_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_params_json.o src/io/register_loader_params_json.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbz.o src/io/register_loader_saver_gbz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbzgraph.o src/io/register_loader_saver_gbzgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gfa.o src/io/register_loader_saver_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/back_translate.o src/unittest/back_translate.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/chain_items.o src/unittest/chain_items.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/component_paths.o src/unittest/component_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/gbwt_extender.o src/unittest/gbwt_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/index_helpers.o src/unittest/index_helpers.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/kff.o src/unittest/kff.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/kmp.o src/unittest/kmp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/locally_expand_graph.o src/unittest/locally_expand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/mem_accelerator.o src/unittest/mem_accelerator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/min_cut_graph.o src/unittest/min_cut_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/protobuf.o src/unittest/protobuf.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/snarl_distance_index.o src/unittest/snarl_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/snarl_seed_clusterer.o src/unittest/snarl_seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/transcriptome.o src/unittest/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/chain_main.o src/subcommand/chain_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/clip_main.o src/subcommand/clip_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/haplotypes_main.o src/subcommand/haplotypes_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_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:147:31: required from here 147 | gs.stream_sort(gam_in, cout, index.get()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/any.h:38, from /usr/include/google/protobuf/generated_message_util.h:52, from /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4: /usr/include/google/protobuf/message_lite.h:381:7: note: declared here 381 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/options.o src/subcommand/options.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/config/allocator_config_jemalloc.o src/config/allocator_config_jemalloc.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/back_translating_alignment_emitter.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/clip.o obj/cluster.o obj/constructor.o obj/contracting_graph.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/explainer.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flat_file_back_translation.o obj/flow_sort.o obj/funnel.o obj/gbwt_extender.o obj/gbwt_helper.o obj/gbwtgraph_helper.o obj/gcsa_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/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/job_schedule.o obj/kff.o obj/kmer.o obj/kmp.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/mem_accelerator.o obj/memoizing_graph.o obj/memusage.o obj/minimizer_mapper.o obj/minimizer_mapper_from_chains.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/recombinator.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarl_distance_index.o obj/snarl_seed_clusterer.o obj/snarls.o obj/source_sink_overlay.o obj/sparse_union_find.o obj/splicing.o obj/split_strand_graph.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/subpath_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_clusters.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/zstdutil.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/back_translate.o obj/algorithms/chain_items.o obj/algorithms/component.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/find_gbwt.o obj/algorithms/find_gbwtgraph.o obj/algorithms/find_translation.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/intersect_path_offsets.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/locally_expand_graph.o obj/algorithms/merge.o obj/algorithms/min_cut_graph.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/pad_band.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/prune_to_connecting_graph.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/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_params_json.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_gbz.o obj/io/register_loader_saver_gbzgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_gfa.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_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++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -o test/build_graph test/build_graph.cpp -Wl,-z,relro -Wl,-z,now lib/libvg.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph -lfastahack -lhts -ltabixpp -lcairo -lm -ldl -lz -lz -lm -lz -lfontconfig -lz -lz -lm -lz -lbrotlicommon -lexpat -lm -lfreetype -lz -lbz2 -lpng16 -lz -lm -lz -lbrotlidec -lbrotlicommon -lX11 -lpthread -lxcb -lXau -lXext -lpthread -lxcb -lXau -lXrender -lX11 -lpthread -lxcb -lXau -lX11 -lpthread -lXau -lxcb -lXau -lxcb-render -lxcb -lXau -lxcb-shm -lxcb -lXau -lXdmcp -lpixman-1 -lm -pthread -lzstd -pthread -rdynamic -ldw -lelf -latomic "-lboost_program_options""" -ldl -llzma -lzstd /usr/lib/x86_64-linux-gnu/libjemalloc.a -Wl,-Bstatic -lvgio -lhts -ldeflate -lz -llzma -lprotobuf -lz -ljansson -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -o bin/vg-ssse3 obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/back_translate.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/chain_items.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/component_paths.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/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gbwt_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_helpers.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/kff.o obj/unittest/kmp.o obj/unittest/locally_expand_graph.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/mem_accelerator.o obj/unittest/min_cut_graph.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/protobuf.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/sequence_complexity.o obj/unittest/snarl_distance_index.o obj/unittest/snarl_seed_clusterer.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.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/transcriptome.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/chain_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/clip_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/haplotypes_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/options.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_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/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 obj/config/allocator_config_jemalloc.o -Wl,-z,relro -Wl,-z,now lib/libvg.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph -lfastahack -lhts -ltabixpp -lcairo -lm -ldl -lz -lz -lm -lz -lfontconfig -lz -lz -lm -lz -lbrotlicommon -lexpat -lm -lfreetype -lz -lbz2 -lpng16 -lz -lm -lz -lbrotlidec -lbrotlicommon -lX11 -lpthread -lxcb -lXau -lXext -lpthread -lxcb -lXau -lXrender -lX11 -lpthread -lxcb -lXau -lX11 -lpthread -lXau -lxcb -lXau -lxcb-render -lxcb -lXau -lxcb-shm -lxcb -lXau -lXdmcp -lpixman-1 -lm -pthread -lzstd -pthread -rdynamic -ldw -lelf -latomic "-lboost_program_options""" -ldl -llzma -lzstd /usr/lib/x86_64-linux-gnu/libjemalloc.a -Wl,-Bstatic -lvgio -lhts -ldeflate -lz -llzma -lprotobuf -lz -ljansson -Wl,-Bdynamic -lpthread -lm make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC CXXFLAGS are -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp LDFLAGS are -Wl,-z,relro -Wl,-z,now rm -f -r bin/unittest rm -f -r lib rm -f -r obj/unittest/support rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/pic/io rm -f -r obj/io rm -f -r obj/pic/algorithms rm -f -r obj/algorithms rm -f -r obj/config rm -f -r obj/pic rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd C && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' rm -rf ../bin ../lib make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' cd externalTools && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' rm -rf bin lib obj rm -f *.o *.a build_gcsa convert_graph gcsa_format try_extend cd benchmark && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2/benchmark' rm -f count_kmers query_gcsa csa_builder csa_query *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2/benchmark' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' cd ./deps && cd gbwt && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' rm -rf bin lib obj rm -f *.o *.a build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' rm -f test_bwtmerge test_metadata test_queries test_support test_variants *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' cd ./deps && cd gbwtgraph && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' rm -rf bin lib obj rm -f *.o *.a gfa2gbwt cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' rm -f test_utils test_gbwtgraph test_cached_gbwtgraph test_gfa test_gbz test_minimizer test_index test_algorithms test_path_cover *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' cd ./deps && cd kff-cpp-api && rm -Rf build cd ./deps && cd gssw && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' rm -f -r lib/ rm -f -r bin/ rm -f -r obj/ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' cd ./deps && cd ssw && cd src && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' rm -f ssw.o ssw_cpp.o ssw_test libssw.so example_c example_cpp libsswjni.so ssw.jar ssw/Aligner.class ssw/Alignment.class ssw/Example.class *~ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' cd ./deps && cd progress_bar && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/progress_bar' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from '/nonexistent/first-build/lib' and '/nonexistent/first-build/include' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 CMakeFiles/uninstall-sdsl.dir/all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/depend make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles/uninstall-sdsl.dir/DependInfo.cmake "--color=" make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f CMakeFiles/uninstall-sdsl.dir/build.make CMakeFiles/uninstall-sdsl.dir/build make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -P /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeModules/cmake_uninstall.cmake -- Looking for "/build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig/sdsl-lite.pc" - not found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vector_il.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vectors.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bits.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_g.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_gg.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_comma.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_delta.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_gamma.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_fibonacci.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/config.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_bwt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_config.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_isa.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa_se.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_alphabet_strategy.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_bitcompressed.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sampling_strategy.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_wt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_fully.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_iterators.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sct3.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/dac_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/enc_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/fast_cache.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/hyb_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_buffer.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_io_wrappers.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_mapper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/inv_perm_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/io.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/iterators.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_bitcompressed.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_byte.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_dac.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree2.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_vlc.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_wt.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/louds_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/memory_management.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/nn_dict_dynamic.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/qsufsort.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_filebuf.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_fs.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_scan.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v5.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/raster_img.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rle_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sada.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sct.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support_sparse_table.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector_15.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sd_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sdsl_concepts.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_mcl.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_scan.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sfstream.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/simple_sds.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_int_stack.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_multi_stack_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_stack_support.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/structure_tree.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_arrays.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_trees.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint128_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint256_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uintx_t.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/util.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/vectors.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/vlc_vector.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wavelet_trees.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wm_int.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_algorithm.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_ap.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_blcd.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_gmr.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_helper.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_huff.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_hutu.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_int.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_pc.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_rlmn.hpp" - found -- Looking for "/build/reproducible-path/vg-1.59.0+ds/lib/libsdsl.a" - not found -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vector_il.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vectors.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bits.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_g.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_gg.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_comma.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_delta.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_gamma.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_fibonacci.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/config.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_bwt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_config.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_isa.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa_se.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_alphabet_strategy.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_bitcompressed.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sampling_strategy.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_wt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_fully.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_iterators.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sct3.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/dac_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/enc_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/fast_cache.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/hyb_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_buffer.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_io_wrappers.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_mapper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/inv_perm_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/io.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/iterators.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_bitcompressed.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_byte.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_dac.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree2.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_vlc.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_wt.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/louds_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/memory_management.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/nn_dict_dynamic.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/qsufsort.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_filebuf.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_fs.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_scan.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v5.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/raster_img.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rle_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sada.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sct.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support_sparse_table.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector_15.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sd_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sdsl_concepts.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_mcl.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_scan.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sfstream.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/simple_sds.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_int_stack.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_multi_stack_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_stack_support.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/structure_tree.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_arrays.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_trees.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint128_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint256_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/uintx_t.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/util.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/vectors.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/vlc_vector.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wavelet_trees.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wm_int.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_algorithm.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_ap.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_blcd.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_gmr.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_helper.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_huff.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_hutu.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_int.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_pc.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Uninstalling "/build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_rlmn.hpp" CMake Warning (dev) at CMakeModules/cmake_uninstall.cmake:24 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Built target uninstall-sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Installed sdsl files were removed. cd ./deps && cd sha1 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sha1' rm -f demo_sha1 test_sha1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sha1' cd ./deps && cd structures && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' cd ./deps && cd sublinear-Li-Stephens && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' rm -f /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' cd ./deps && cd libhandlegraph && rm -Rf build CMakeCache.txt CMakeFiles cd ./deps && cd libvgio && rm -Rf build CMakeCache.txt CMakeFiles # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' make -j42 "INSTALL=install --strip-program=true" SFX=-sse3 all test/build_graph bin/shuf make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC CXXFLAGS are -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp LDFLAGS are -Wl,-z,relro -Wl,-z,now . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp" ./install.sh /build/reproducible-path/vg-1.59.0+ds . ./source_me.sh && cd deps/ssw/src && make && ar rs /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a ssw.o ssw_cpp.o && cp ssw_cpp.h ssw.h /build/reproducible-path/vg-1.59.0+ds/include . ./source_me.sh && cd deps/libhandlegraph && rm -Rf build CMakeCache.txt CMakeFiles && mkdir build && cd build && CXXFLAGS="-std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make && make install . ./source_me.sh && cd deps/kff-cpp-api && rm -Rf build && mkdir build && cd build && cmake .. && make && cp kff_io.hpp /build/reproducible-path/vg-1.59.0+ds/include && mv libkff.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && cd deps/gssw && make && cp lib/libgssw.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp src/gssw.h /build/reproducible-path/vg-1.59.0+ds/include/ . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/reproducible-path/vg-1.59.0+ds/include" make libs && cp lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/lib/ && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS && cp src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp -r src/include/structures /build/reproducible-path/vg-1.59.0+ds/include/ rm -f lib/cleaned_old_protobuf* make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' gcc -c -o ssw.o ssw.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -pipe -O3 -I. g++ -c -o ssw_cpp.o ssw_cpp.cpp -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -pipe -O3 -I. gcc -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' Library will be installed in '/build/reproducible-path/vg-1.59.0+ds' gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd externalTools && make all cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi rm -f /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/* WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. if [ ! -d obj ]; then mkdir -p obj; fi rm -Rf include/google/protobuf deps/protobuf make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make all if [ ! -d lib ]; then mkdir -p lib; fi cd quicktree_1.1 && make all CC="gcc -std=c99" make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' touch lib/cleaned_old_protobuf_v003 find bin obj lib -type f -delete make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj; fi gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c if [ ! -d obj ]; then mkdir -p obj; fi gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test; fi if [ ! -d lib ]; then mkdir -p lib; fi . ./source_me.sh && g++ -I -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/progress_bar.o deps/progress_bar/progress_bar.cpp g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/union_find.cpp -o obj/union_find.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o make[2]: 'bin/shuf' is up to date. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -- The C compiler identification is GNU 14.2.0 -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ src/gssw.c: In function ‘gssw_graph_print’: src/gssw.c:1947:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1947 | fprintf(stdout, "GRAPH // node %llu %u %s\n", n->id, n->len, n->seq); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c:1951:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1951 | fprintf(stdout, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c:1951:56: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1951 | fprintf(stdout, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c: In function ‘gssw_graph_print_stderr’: src/gssw.c:1963:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1963 | fprintf(stderr, "GRAPH // node %llu %u %s\n", n->id, n->len, n->seq); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c:1967:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1967 | fprintf(stderr, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c:1967:56: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1967 | fprintf(stderr, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c: In function ‘gssw_graph_print_score_matrices’: src/gssw.c:1978:31: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1978 | fprintf(out, "node %llu\n", n->id); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu -- The CXX compiler identification is GNU 14.2.0 src/gssw.c: In function ‘gssw_print_graph_cigar’: -- Detecting C compiler ABI info src/gssw.c:3623:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 3623 | fprintf(out, "%llu[", nc->node->id); | ~~~^ ~~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu -- The CXX compiler identification is GNU 14.2.0 src/gssw.c: In function ‘gssw_create_seed_byte’: src/gssw.c:5095:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5095 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); | ~~~^ ~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c: In function ‘gssw_create_seed_word’: -- Detecting C compiler ABI info src/gssw.c:5130:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5130 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); | ~~~^ ~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu -- The C compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- Detecting C compiler ABI info - done ar rc cuTest.a *.o ranlib cuTest.a -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' -- Detecting C compiler ABI info - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting CXX compiler ABI info -- Detecting C compiler ABI info /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ -- Detecting CXX compiler ABI info - done -- Detecting C compiler ABI info - done -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done libhandlegraph is root project or external_project -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Configuring done (0.7s) -- Detecting C compile features - done -- Compiler is recent enough to support C++14. -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build -- Configuring done (0.7s) make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f 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CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 2%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c 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object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o [ 42%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dfs.cpp make[5]: Entering directory 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-ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP 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CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/copy_graph.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/append_graph.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/are_equivalent.cpp [ 65%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp [ 71%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o [ 71%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_tips.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/topological_sort.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 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-ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp -- Performing Test 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-I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_acyclic.cpp gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm [ 82%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/reverse_complement.cpp -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' [ 85%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o cd C && make all /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/split_strands.cpp make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+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 cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h [ 88%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/chop.cpp cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp 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 cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h [ 91%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h [ 94%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/extend.cpp cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h -- Performing Test HAVE_CXA_DEMANGLE mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -o ssw_test ssw.o main.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -pipe -O3 -I. -lm -lz 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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -I inc -I ../lib/ -c impl/*.c gcc -o example_c ssw.o example.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -pipe -O3 -I. -lm -lz 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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' g++ -o example_cpp example.cpp ssw.o ssw_cpp.o -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -pipe -O3 -I. -lm -lz cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:102 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio -- Looking for C++ include cstdio - found 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)) { | ^ -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot src/gssw.c: In function ‘gssw_sw_software_byte’: src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 277 | memcpy(scratch, to_unswizzle, size); | ^ In function ‘unswizzle_byte’, inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Configuring done (2.6s) make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' ar: creating /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a -- Generating done (0.2s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 8 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_config.cpp [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bits.cpp [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/config.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_isa.cpp [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa.cpp [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/io.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/louds_tree.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/memory_management.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_fs.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sd_vector.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sfstream.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o -MF CMakeFiles/sdsl.dir/simple_sds.cpp.o.d -o CMakeFiles/sdsl.dir/simple_sds.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/simple_sds.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/structure_tree.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint128_t.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/wt_helper.cpp src/gssw.c: In function ‘gssw_sw_software_word’: src/gssw.c:1117:5: warning: ‘__builtin_memcpy’ writing between 18446744069414584336 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 1117 | memcpy(scratch, to_unswizzle, size * sizeof(int16_t)); | ^ In function ‘unswizzle_word’, inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/vector:63, from /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:8: In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = long int]’, inlined from ‘static void std::allocator_traits >::deallocate(allocator_type&, pointer, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:544:23, inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:389:19, inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:368:15, inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:738:7, inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:445:5: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: ‘void operator delete(void*, std::size_t)’ called on pointer ‘’ with nonzero offset [1, 9223372036854775800] [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = long int]’, inlined from ‘static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:509:28, inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:398:44, inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:334:26, inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const value_type&, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:571:47, inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:327:85: /usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from ‘void* operator new(std::size_t)’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4975:5: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 4975 | strncpy(n->seq, seq, len); n->seq[len] = 0; | ^ src/gssw.c:4971:19: note: length computed here 4971 | int32_t len = strlen(seq); | ^~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 33%] Linking CXX static library libkff.a 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 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 33%] Built target kff make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' In file included from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1358:27, inlined from ‘void sdsl::int_vector< >::resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:380:23, inlined from ‘sdsl::int_vector< >::int_vector(size_type, value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1285:11, inlined from ‘sdsl::excess::impl::impl()’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:448:9: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 448 | *word &= | ^~~~~ [ 66%] Building CXX object benchmarks/CMakeFiles/reader_bench.dir/reader.cpp.o [ 66%] Building CXX object CMakeFiles/kff_example.dir/main.cpp.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 impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:765:75: note: declared here 765 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:773:68: note: declared here 773 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:774:68: note: declared here 774 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ar rc /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o [ 83%] Linking CXX executable reader_bench ranlib /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a impl/sonLibConnectivity.c: In function ‘stConnectivity_addEdge’: impl/sonLibConnectivity.c:248:33: warning: pointer ‘component1’ may be used after ‘free’ [-Wuse-after-free] 248 | connectivity->mergeCallback(connectivity->mergeExtraData, component1, component2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘stConnectedComponent_destruct’, inlined from ‘stConnectivity_addEdge’ at impl/sonLibConnectivity.c:238:3: impl/sonLibConnectivity.c:608:9: note: call to ‘free’ here 608 | free(comp); | ^~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 83%] Built target reader_bench make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o [100%] Linking CXX executable kff_example 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-1.59.0+ds/deps/kff-cpp-api/build' [100%] Built target kff_example make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibTreap.c: In function ‘stTreap_remove’: impl/sonLibTreap.c:331:18: warning: pointer ‘rmnode’ used after ‘free’ [-Wuse-after-free] 331 | stTreap *p = rmnode->parent; | ^ impl/sonLibTreap.c:329:9: note: call to ‘free’ here 329 | free(rmnode); | ^~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 94%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Linking CXX static library libhandlegraph.a [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/g++ -fPIC -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,--dependency-file,CMakeFiles/handlegraph_shared.dir/link.d -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/dfs.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_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.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/mutable_path_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/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Built target handlegraph_shared /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.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_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.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/mutable_path_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/chop.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-1.59.0+ds/deps/libhandlegraph/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Built target handlegraph_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 94%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 97%] Built target handlegraph_shared [100%] Built target handlegraph_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.a -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_metadata.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_metadata.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_position_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/util.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/buildable_snarl_decomposition.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/trivially_serializable.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/iteratee.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_tips.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/count_walks.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/split_strands.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/eades_algorithm.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/are_equivalent.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dijkstra.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/append_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/apply_orientations.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal/dfs.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dagify.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/reverse_complement.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_shortest_paths.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/topological_sort.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/copy_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/strongly_connected_components.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/chop.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/extend.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/weakly_connected_components.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_single_stranded.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_acyclic.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/snarl_decomposition.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/types.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/named_node_back_translation.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphConfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphConfigVersion.cmake make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' rm -f /build/reproducible-path/vg-1.59.0+ds/include/vg.pb.h /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp" && export LDFLAGS="-Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && rm -rf build-vg && mkdir build-vg && cd build-vg && PKG_CONFIG_PATH=/build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig: cmake -DCMAKE_CXX_STANDARD=14 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH="/usr;/" -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make clean && VERBOSE=1 make && make install -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") Building libvgio for C++ 14 -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Could NOT find Protobuf (missing: Protobuf_DIR) No installed Protobuf has registered itself with CMake. -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.21.12") Found Protobuf using FindProtobuf.cmake -- Found Threads: TRUE Using real Threads library -- Checking for module 'htslib' -- Found htslib, version 1.20 -- Checking for module 'jansson' -- Found jansson, version 2.14 [100%] Linking CXX static library libsdsl.a cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 Using installed libhandlegraph -- Configuring done (0.8s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make -f CMakeFiles/test_libvgio.dir/build.make CMakeFiles/test_libvgio.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/test_libvgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 0%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 2%] Running cpp protocol buffer compiler on deps/vg.proto [ 5%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" 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-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 14%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o [ 14%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o [ 14%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o [ 23%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o [ 23%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o [ 23%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o [ 29%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o [ 29%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o [ 32%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/vg.pb.cc.o -MF CMakeFiles/vgio_static.dir/vg.pb.cc.o.d -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/vg.pb.cc [ 35%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 38%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 41%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/hfile_cppstream.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/edit.cpp.o -MF CMakeFiles/vgio_static.dir/src/edit.cpp.o.d -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/edit.cpp /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/json2pb.cpp /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c 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CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_io.cpp [ 52%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o [ 52%] Building CXX object 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-Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream_multiplexer.cpp /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/vpkg.cpp /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/simple_sds.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 /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Built target sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/reproducible-path/vg-1.59.0+ds/include/sdsl/*' rm -f '/build/reproducible-path/vg-1.59.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" 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-1.59.0+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-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp Install the project... /usr/bin/cmake -P cmake_install.cmake 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 -- Install configuration: "Release" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bits.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/config.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/io.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/iterators.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/raster_img.hpp ranlib sonLib.a -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rle_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/simple_sds.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/util.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/vectors.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libsdsl.a rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/reproducible-path/vg-1.59.0+ds/include'. The library files are located in '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include/ && cd deps/gcsa2 && make directories && make lib/libgcsa2.a && mv lib/libgcsa2.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwt && make clean && make && mv lib/libgbwt.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/reproducible-path/vg-1.59.0+ds/include:/build/reproducible-path/vg-1.59.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp" make && cp lib/libbdsg.a /build/reproducible-path/vg-1.59.0+ds/lib && cp -r bdsg/include/* /build/reproducible-path/vg-1.59.0+ds/include rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' rm -rf bin lib obj mkdir -p bin mkdir -p lib mkdir -p obj rm -f *.o *.a build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' [ ! -e bdsg/obj ] || rm -r bdsg/obj cd tests && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dbg.o src/dbg.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gcsa.o src/gcsa.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp rm -f test_bwtmerge test_metadata test_queries test_support test_variants *.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/lcp.o src/lcp.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_graph.o src/path_graph.cpp make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' [ ! -e lib ] || rm -r lib /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' mkdir -p bin [ ! -e bin ] || rm -r bin make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' mkdir -p lib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' mkdir -p obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/mapped_structs.cpp -o bdsg/obj/mapped_structs.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/bwtmerge.o src/bwtmerge.cpp mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwt.o src/cached_gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/reference_path_overlay.cpp -o bdsg/obj/reference_path_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_reference_path_overlay.cpp -o bdsg/obj/packed_reference_path_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/path_subgraph_overlay.cpp -o bdsg/obj/path_subgraph_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/subgraph_overlay.cpp -o bdsg/obj/subgraph_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dynamic_gbwt.o src/dynamic_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/fast_locate.o src/fast_locate.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwt.o src/gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata.o src/metadata.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/test.o src/test.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/variants.o src/variants.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_gbwt.o src/build_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_ri.o src/build_ri.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/merge_gbwt.o src/merge_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/benchmark.o src/benchmark.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata_tool.o src/metadata_tool.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp mv ../bin/sonLibTests.tmp ../bin/sonLibTests make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sonLib' . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/reproducible-path/vg-1.59.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/reproducible-path/vg-1.59.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/reproducible-path/vg-1.59.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c ar rc 3EdgeConnected.a *.o ranlib 3EdgeConnected.a [ 97%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wl,--dependency-file,CMakeFiles/vgio.dir/link.d -Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib -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 /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 97%] Built target vgio [100%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I .//../sonLib/lib/ -c impl/*.c gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 /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-1.59.0+ds/deps/libvgio/build-vg' [100%] Built target vgio_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 0%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [100%] Built target vgio [100%] Built target vgio_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libvgio.so -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libvgio.a -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/vg -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/loader.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/json2pb.h -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/registry.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/edit.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' ar rcs lib/libgbwt.a obj/algorithms.o obj/bwtmerge.o obj/cached_gbwt.o obj/dynamic_gbwt.o obj/fast_locate.o obj/files.o obj/gbwt.o obj/internal.o obj/metadata.o obj/support.o obj/test.o obj/utils.o obj/variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_gbwt obj/build_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_ri obj/build_ri.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/merge_gbwt obj/merge_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/benchmark obj/benchmark.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/metadata_tool obj/metadata_tool.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/remove_seq obj/remove_seq.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 rm obj/build_ri.o obj/metadata_tool.o obj/benchmark.o obj/merge_gbwt.o obj/remove_seq.o obj/build_gbwt.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv lib/libgbwtgraph.a /build/reproducible-path/vg-1.59.0+ds/lib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' rm -rf bin lib obj rm -f *.o *.a gfa2gbwt cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' rm -f test_utils test_gbwtgraph test_cached_gbwtgraph test_gfa test_gbz test_minimizer test_index test_algorithms test_path_cover *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' mkdir -p bin mkdir -p lib mkdir -p obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwtgraph.o src/cached_gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwtgraph.o src/gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz.o src/gbz.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa.o src/gfa.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/minimizer.o src/minimizer.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_cover.o src/path_cover.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa2gbwt.o src/gfa2gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz_stats.o src/gbz_stats.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/kmer_freq.o src/kmer_freq.cpp 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/mapped_structs.o bdsg/obj/packed_graph.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/reference_path_overlay.o bdsg/obj/packed_reference_path_overlay.o bdsg/obj/path_subgraph_overlay.o bdsg/obj/subgraph_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/snarl_distance_index.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' ar rcs lib/libgcsa2.a obj/algorithms.o obj/dbg.o obj/files.o obj/gcsa.o obj/internal.o obj/lcp.o obj/path_graph.o obj/support.o obj/utils.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a ar rcs lib/libgbwtgraph.a obj/algorithms.o obj/cached_gbwtgraph.o obj/gbwtgraph.o obj/gbz.o obj/gfa.o obj/internal.o obj/minimizer.o obj/path_cover.o obj/utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/gfa2gbwt obj/gfa2gbwt.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/gbz_stats obj/gbz_stats.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/kmer_freq obj/kmer_freq.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 rm obj/kmer_freq.o obj/gbz_stats.o obj/gfa2gbwt.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/back_translating_alignment_emitter.o src/back_translating_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/clip.o src/clip.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/contracting_graph.o src/contracting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/explainer.o src/explainer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/flat_file_back_translation.o src/flat_file_back_translation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/gbwt_extender.o src/gbwt_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/gbwtgraph_helper.o src/gbwtgraph_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/gcsa_helper.o src/gcsa_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/job_schedule.o src/job_schedule.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/kff.o src/kff.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/kmp.o src/kmp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/mem_accelerator.o src/mem_accelerator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/minimizer_mapper_from_chains.o src/minimizer_mapper_from_chains.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/recombinator.o src/recombinator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/snarl_distance_index.o src/snarl_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/snarl_seed_clusterer.o src/snarl_seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/sparse_union_find.o src/sparse_union_find.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subpath_overlay.o src/subpath_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/traversal_clusters.o src/traversal_clusters.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/zstdutil.o src/zstdutil.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/back_translate.o src/algorithms/back_translate.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/chain_items.o src/algorithms/chain_items.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/component.o src/algorithms/component.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/find_gbwt.o src/algorithms/find_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/find_gbwtgraph.o src/algorithms/find_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/find_translation.o src/algorithms/find_translation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/intersect_path_offsets.o src/algorithms/intersect_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/locally_expand_graph.o src/algorithms/locally_expand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/min_cut_graph.o src/algorithms/min_cut_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/pad_band.o src/algorithms/pad_band.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/prune_to_connecting_graph.o src/algorithms/prune_to_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_params_json.o src/io/register_loader_params_json.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbz.o src/io/register_loader_saver_gbz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbzgraph.o src/io/register_loader_saver_gbzgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gfa.o src/io/register_loader_saver_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/back_translate.o src/unittest/back_translate.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/chain_items.o src/unittest/chain_items.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/component_paths.o src/unittest/component_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/gbwt_extender.o src/unittest/gbwt_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/index_helpers.o src/unittest/index_helpers.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/kff.o src/unittest/kff.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/kmp.o src/unittest/kmp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/locally_expand_graph.o src/unittest/locally_expand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/mem_accelerator.o src/unittest/mem_accelerator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/min_cut_graph.o src/unittest/min_cut_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/protobuf.o src/unittest/protobuf.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/snarl_distance_index.o src/unittest/snarl_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/snarl_seed_clusterer.o src/unittest/snarl_seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/transcriptome.o src/unittest/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/chain_main.o src/subcommand/chain_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/clip_main.o src/subcommand/clip_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/haplotypes_main.o src/subcommand/haplotypes_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_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:147:31: required from here 147 | gs.stream_sort(gam_in, cout, index.get()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/any.h:38, from /usr/include/google/protobuf/generated_message_util.h:52, from /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4: /usr/include/google/protobuf/message_lite.h:381:7: note: declared here 381 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/options.o src/subcommand/options.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/config/allocator_config_jemalloc.o src/config/allocator_config_jemalloc.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/back_translating_alignment_emitter.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/clip.o obj/cluster.o obj/constructor.o obj/contracting_graph.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/explainer.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flat_file_back_translation.o obj/flow_sort.o obj/funnel.o obj/gbwt_extender.o obj/gbwt_helper.o obj/gbwtgraph_helper.o obj/gcsa_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/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/job_schedule.o obj/kff.o obj/kmer.o obj/kmp.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/mem_accelerator.o obj/memoizing_graph.o obj/memusage.o obj/minimizer_mapper.o obj/minimizer_mapper_from_chains.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/recombinator.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarl_distance_index.o obj/snarl_seed_clusterer.o obj/snarls.o obj/source_sink_overlay.o obj/sparse_union_find.o obj/splicing.o obj/split_strand_graph.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/subpath_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_clusters.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/zstdutil.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/back_translate.o obj/algorithms/chain_items.o obj/algorithms/component.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/find_gbwt.o obj/algorithms/find_gbwtgraph.o obj/algorithms/find_translation.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/intersect_path_offsets.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/locally_expand_graph.o obj/algorithms/merge.o obj/algorithms/min_cut_graph.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/pad_band.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/prune_to_connecting_graph.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/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_params_json.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_gbz.o obj/io/register_loader_saver_gbzgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_gfa.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_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++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -o test/build_graph test/build_graph.cpp -Wl,-z,relro -Wl,-z,now lib/libvg.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph -lfastahack -lhts -ltabixpp -lcairo -lm -ldl -lz -lz -lm -lz -lfontconfig -lz -lz -lm -lz -lbrotlicommon -lexpat -lm -lfreetype -lz -lbz2 -lpng16 -lz -lm -lz -lbrotlidec -lbrotlicommon -lX11 -lpthread -lxcb -lXau -lXext -lpthread -lxcb -lXau -lXrender -lX11 -lpthread -lxcb -lXau -lX11 -lpthread -lXau -lxcb -lXau -lxcb-render -lxcb -lXau -lxcb-shm -lxcb -lXau -lXdmcp -lpixman-1 -lm -pthread -lzstd -pthread -rdynamic -ldw -lelf -latomic "-lboost_program_options""" -ldl -llzma -lzstd /usr/lib/x86_64-linux-gnu/libjemalloc.a -Wl,-Bstatic -lvgio -lhts -ldeflate -lz -llzma -lprotobuf -lz -ljansson -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -o bin/vg-sse3 obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/back_translate.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/chain_items.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/component_paths.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/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gbwt_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_helpers.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/kff.o obj/unittest/kmp.o obj/unittest/locally_expand_graph.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/mem_accelerator.o obj/unittest/min_cut_graph.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/protobuf.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/sequence_complexity.o obj/unittest/snarl_distance_index.o obj/unittest/snarl_seed_clusterer.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.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/transcriptome.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/chain_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/clip_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/haplotypes_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/options.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_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/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 obj/config/allocator_config_jemalloc.o -Wl,-z,relro -Wl,-z,now lib/libvg.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph -lfastahack -lhts -ltabixpp -lcairo -lm -ldl -lz -lz -lm -lz -lfontconfig -lz -lz -lm -lz -lbrotlicommon -lexpat -lm -lfreetype -lz -lbz2 -lpng16 -lz -lm -lz -lbrotlidec -lbrotlicommon -lX11 -lpthread -lxcb -lXau -lXext -lpthread -lxcb -lXau -lXrender -lX11 -lpthread -lxcb -lXau -lX11 -lpthread -lXau -lxcb -lXau -lxcb-render -lxcb -lXau -lxcb-shm -lxcb -lXau -lXdmcp -lpixman-1 -lm -pthread -lzstd -pthread -rdynamic -ldw -lelf -latomic "-lboost_program_options""" -ldl -llzma -lzstd /usr/lib/x86_64-linux-gnu/libjemalloc.a -Wl,-Bstatic -lvgio -lhts -ldeflate -lz -llzma -lprotobuf -lz -ljansson -Wl,-Bdynamic -lpthread -lm make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3" dh_auto_build -- SFX=-plain all test/build_graph bin/shuf make -j42 "INSTALL=install --strip-program=true" SFX=-plain all test/build_graph bin/shuf make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC CXXFLAGS are -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp LDFLAGS are -Wl,-z,relro -Wl,-z,now . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" ./install.sh /build/reproducible-path/vg-1.59.0+ds Library will be installed in '/build/reproducible-path/vg-1.59.0+ds' WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. make[2]: 'bin/shuf' is up to date. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The CXX compiler identification is GNU 14.2.0 -- The C compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- 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++14. -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success -- Performing Test HAVE_CXA_DEMANGLE -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:102 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio -- Looking for C++ include cstdio - found -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -- Configuring done (1.4s) -- Generating done (0.2s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 8 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bits.cpp [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/config.cpp [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa.cpp [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_isa.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_config.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/memory_management.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/io.cpp [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_fs.cpp [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/louds_tree.cpp [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sd_vector.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sfstream.cpp [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o -MF CMakeFiles/sdsl.dir/simple_sds.cpp.o.d -o CMakeFiles/sdsl.dir/simple_sds.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/simple_sds.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/structure_tree.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/wt_helper.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint128_t.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp In file included from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1358:27, inlined from ‘void sdsl::int_vector< >::resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:380:23, inlined from ‘sdsl::int_vector< >::int_vector(size_type, value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1285:11, inlined from ‘sdsl::excess::impl::impl()’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:448:9: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 448 | *word &= | ^~~~~ [100%] Linking CXX static library libsdsl.a cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/vg-1.59.0+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/simple_sds.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 /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/reproducible-path/vg-1.59.0+ds/include/sdsl/*' rm -f '/build/reproducible-path/vg-1.59.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+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-1.59.0+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-1.59.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bits.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/config.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/io.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/iterators.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rle_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/simple_sds.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/util.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/vectors.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libsdsl.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/reproducible-path/vg-1.59.0+ds/include'. The library files are located in '/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include/ && cd deps/gcsa2 && make directories && make lib/libgcsa2.a && mv lib/libgcsa2.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwt && make clean && make && mv lib/libgbwt.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/reproducible-path/vg-1.59.0+ds/include:/build/reproducible-path/vg-1.59.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" make && cp lib/libbdsg.a /build/reproducible-path/vg-1.59.0+ds/lib && cp -r bdsg/include/* /build/reproducible-path/vg-1.59.0+ds/include rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' make[3]: Nothing to be done for 'directories'. make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' rm -rf bin lib obj make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' [ ! -e bdsg/obj ] || rm -r bdsg/obj ar rcs lib/libgcsa2.a obj/algorithms.o obj/dbg.o obj/files.o obj/gcsa.o obj/internal.o obj/lcp.o obj/path_graph.o obj/support.o obj/utils.o [ ! -e lib ] || rm -r lib rm -f *.o *.a build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq [ ! -e bin ] || rm -r bin cd tests && make clean make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' rm -f test_bwtmerge test_metadata test_queries test_support test_variants *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' mkdir -p bin mkdir -p lib g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o mkdir -p obj g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/bwtmerge.o src/bwtmerge.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/mapped_structs.cpp -o bdsg/obj/mapped_structs.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwt.o src/cached_gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dynamic_gbwt.o src/dynamic_gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/fast_locate.o src/fast_locate.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/reference_path_overlay.cpp -o bdsg/obj/reference_path_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwt.o src/gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_reference_path_overlay.cpp -o bdsg/obj/packed_reference_path_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/path_subgraph_overlay.cpp -o bdsg/obj/path_subgraph_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata.o src/metadata.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/subgraph_overlay.cpp -o bdsg/obj/subgraph_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/test.o src/test.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/variants.o src/variants.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_gbwt.o src/build_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_ri.o src/build_ri.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/merge_gbwt.o src/merge_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/benchmark.o src/benchmark.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata_tool.o src/metadata_tool.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' ar rcs lib/libgbwt.a obj/algorithms.o obj/bwtmerge.o obj/cached_gbwt.o obj/dynamic_gbwt.o obj/fast_locate.o obj/files.o obj/gbwt.o obj/internal.o obj/metadata.o obj/support.o obj/test.o obj/utils.o obj/variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_gbwt obj/build_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_ri obj/build_ri.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/merge_gbwt obj/merge_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/benchmark obj/benchmark.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/metadata_tool obj/metadata_tool.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+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-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/remove_seq obj/remove_seq.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 rm obj/build_ri.o obj/metadata_tool.o obj/benchmark.o obj/merge_gbwt.o obj/remove_seq.o obj/build_gbwt.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv lib/libgbwtgraph.a /build/reproducible-path/vg-1.59.0+ds/lib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' rm -rf bin lib obj rm -f *.o *.a gfa2gbwt cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' rm -f test_utils test_gbwtgraph test_cached_gbwtgraph test_gfa test_gbz test_minimizer test_index test_algorithms test_path_cover *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' mkdir -p bin mkdir -p lib mkdir -p obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwtgraph.o src/cached_gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwtgraph.o src/gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz.o src/gbz.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa.o src/gfa.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/minimizer.o src/minimizer.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_cover.o src/path_cover.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa2gbwt.o src/gfa2gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz_stats.o src/gbz_stats.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/kmer_freq.o src/kmer_freq.cpp 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/mapped_structs.o bdsg/obj/packed_graph.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/reference_path_overlay.o bdsg/obj/packed_reference_path_overlay.o bdsg/obj/path_subgraph_overlay.o bdsg/obj/subgraph_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/snarl_distance_index.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a ar rcs lib/libgbwtgraph.a obj/algorithms.o obj/cached_gbwtgraph.o obj/gbwtgraph.o obj/gbz.o obj/gfa.o obj/internal.o obj/minimizer.o obj/path_cover.o obj/utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/gfa2gbwt obj/gfa2gbwt.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/gbz_stats obj/gbz_stats.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/kmer_freq obj/kmer_freq.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 rm obj/kmer_freq.o obj/gbz_stats.o obj/gfa2gbwt.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/back_translating_alignment_emitter.o src/back_translating_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/clip.o src/clip.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/contracting_graph.o src/contracting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/explainer.o src/explainer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/flat_file_back_translation.o src/flat_file_back_translation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gbwt_extender.o src/gbwt_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gbwtgraph_helper.o src/gbwtgraph_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gcsa_helper.o src/gcsa_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/job_schedule.o src/job_schedule.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/kff.o src/kff.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/kmp.o src/kmp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mem_accelerator.o src/mem_accelerator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/minimizer_mapper_from_chains.o src/minimizer_mapper_from_chains.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/recombinator.o src/recombinator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/snarl_distance_index.o src/snarl_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/snarl_seed_clusterer.o src/snarl_seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/sparse_union_find.o src/sparse_union_find.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subpath_overlay.o src/subpath_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/traversal_clusters.o src/traversal_clusters.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/zstdutil.o src/zstdutil.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/back_translate.o src/algorithms/back_translate.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/chain_items.o src/algorithms/chain_items.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/component.o src/algorithms/component.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/find_gbwt.o src/algorithms/find_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/find_gbwtgraph.o src/algorithms/find_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/find_translation.o src/algorithms/find_translation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/intersect_path_offsets.o src/algorithms/intersect_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/locally_expand_graph.o src/algorithms/locally_expand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/min_cut_graph.o src/algorithms/min_cut_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/pad_band.o src/algorithms/pad_band.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/prune_to_connecting_graph.o src/algorithms/prune_to_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_params_json.o src/io/register_loader_params_json.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbz.o src/io/register_loader_saver_gbz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbzgraph.o src/io/register_loader_saver_gbzgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gfa.o src/io/register_loader_saver_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/back_translate.o src/unittest/back_translate.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/chain_items.o src/unittest/chain_items.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/component_paths.o src/unittest/component_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/gbwt_extender.o src/unittest/gbwt_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/index_helpers.o src/unittest/index_helpers.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/kff.o src/unittest/kff.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/kmp.o src/unittest/kmp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/locally_expand_graph.o src/unittest/locally_expand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mem_accelerator.o src/unittest/mem_accelerator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/min_cut_graph.o src/unittest/min_cut_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/protobuf.o src/unittest/protobuf.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/snarl_distance_index.o src/unittest/snarl_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/snarl_seed_clusterer.o src/unittest/snarl_seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/transcriptome.o src/unittest/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/chain_main.o src/subcommand/chain_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/clip_main.o src/subcommand/clip_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/haplotypes_main.o src/subcommand/haplotypes_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_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:147:31: required from here 147 | gs.stream_sort(gam_in, cout, index.get()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/any.h:38, from /usr/include/google/protobuf/generated_message_util.h:52, from /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4: /usr/include/google/protobuf/message_lite.h:381:7: note: declared here 381 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/options.o src/subcommand/options.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/config/allocator_config_jemalloc.o src/config/allocator_config_jemalloc.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/back_translating_alignment_emitter.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/clip.o obj/cluster.o obj/constructor.o obj/contracting_graph.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/explainer.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flat_file_back_translation.o obj/flow_sort.o obj/funnel.o obj/gbwt_extender.o obj/gbwt_helper.o obj/gbwtgraph_helper.o obj/gcsa_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/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/job_schedule.o obj/kff.o obj/kmer.o obj/kmp.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/mem_accelerator.o obj/memoizing_graph.o obj/memusage.o obj/minimizer_mapper.o obj/minimizer_mapper_from_chains.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/recombinator.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarl_distance_index.o obj/snarl_seed_clusterer.o obj/snarls.o obj/source_sink_overlay.o obj/sparse_union_find.o obj/splicing.o obj/split_strand_graph.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/subpath_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_clusters.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/zstdutil.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/back_translate.o obj/algorithms/chain_items.o obj/algorithms/component.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/find_gbwt.o obj/algorithms/find_gbwtgraph.o obj/algorithms/find_translation.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/intersect_path_offsets.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/locally_expand_graph.o obj/algorithms/merge.o obj/algorithms/min_cut_graph.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/pad_band.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/prune_to_connecting_graph.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/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_params_json.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_gbz.o obj/io/register_loader_saver_gbzgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_gfa.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_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++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -o test/build_graph test/build_graph.cpp -Wl,-z,relro -Wl,-z,now lib/libvg.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph -lfastahack -lhts -ltabixpp -lcairo -lm -ldl -lz -lz -lm -lz -lfontconfig -lz -lz -lm -lz -lbrotlicommon -lexpat -lm -lfreetype -lz -lbz2 -lpng16 -lz -lm -lz -lbrotlidec -lbrotlicommon -lX11 -lpthread -lxcb -lXau -lXext -lpthread -lxcb -lXau -lXrender -lX11 -lpthread -lxcb -lXau -lX11 -lpthread -lXau -lxcb -lXau -lxcb-render -lxcb -lXau -lxcb-shm -lxcb -lXau -lXdmcp -lpixman-1 -lm -pthread -lzstd -pthread -rdynamic -ldw -lelf -latomic "-lboost_program_options""" -ldl -llzma -lzstd /usr/lib/x86_64-linux-gnu/libjemalloc.a -Wl,-Bstatic -lvgio -lhts -ldeflate -lz -llzma -lprotobuf -lz -ljansson -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -o bin/vg-plain obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/back_translate.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/chain_items.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/component_paths.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/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gbwt_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_helpers.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/kff.o obj/unittest/kmp.o obj/unittest/locally_expand_graph.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/mem_accelerator.o obj/unittest/min_cut_graph.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/protobuf.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/sequence_complexity.o obj/unittest/snarl_distance_index.o obj/unittest/snarl_seed_clusterer.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.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/transcriptome.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/chain_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/clip_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/haplotypes_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/options.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_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/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 obj/config/allocator_config_jemalloc.o -Wl,-z,relro -Wl,-z,now lib/libvg.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph -lfastahack -lhts -ltabixpp -lcairo -lm -ldl -lz -lz -lm -lz -lfontconfig -lz -lz -lm -lz -lbrotlicommon -lexpat -lm -lfreetype -lz -lbz2 -lpng16 -lz -lm -lz -lbrotlidec -lbrotlicommon -lX11 -lpthread -lxcb -lXau -lXext -lpthread -lxcb -lXau -lXrender -lX11 -lpthread -lxcb -lXau -lX11 -lpthread -lXau -lxcb -lXau -lxcb-render -lxcb -lXau -lxcb-shm -lxcb -lXau -lXdmcp -lpixman-1 -lm -pthread -lzstd -pthread -rdynamic -ldw -lelf -latomic "-lboost_program_options""" -ldl -llzma -lzstd /usr/lib/x86_64-linux-gnu/libjemalloc.a -Wl,-Bstatic -lvgio -lhts -ldeflate -lz -llzma -lprotobuf -lz -ljansson -Wl,-Bdynamic -lpthread -lm make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' cp bin/vg-plain debian/help/vg PATH=$PATH:/build/reproducible-path/vg-1.59.0+ds/debian/help \ LD_PRELOAD= 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-1.59.0+ds' debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_build -- docs make -j42 "INSTALL=install --strip-program=true" docs make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC CXXFLAGS are -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp LDFLAGS are -Wl,-z,relro -Wl,-z,now 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 'HTML_TIMESTAMP' at line 1136 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 'FORMULA_TRANSPARENT' at line 1417 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 'LATEX_SOURCE_CODE' at line 1702 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 'RTF_SOURCE_CODE' at line 1776 of file 'Doxyfile' has become obsolete. 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To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_FONTSIZE' at line 2125 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 'DOT_TRANSPARENT' at line 2338 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 'src/unittest/driver.cpp' does not exist warning: tag INPUT: input source 'src/unittest/driver.hpp' does not exist 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 'src/unittest/driver.cpp' is not a readable file or directory... skipping. warning: source 'src/unittest/driver.hpp' is not a readable file or directory... skipping. 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: 1.9.8 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-1.59.0+ds/src Searching for files in directory /build/reproducible-path/vg-1.59.0+ds/src/algorithms Searching for files in directory /build/reproducible-path/vg-1.59.0+ds/src/io Searching for files in directory /build/reproducible-path/vg-1.59.0+ds/src/subcommand Searching for files in directory /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src Searching for files in directory /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph Searching for files in directory /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src Searching for files in directory /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io Searching for files in directory /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps Reading and parsing tag files Parsing files Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/aligner.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/aligner.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/aligner.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/aligner.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/alignment.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/alignment.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/alignment.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/alignment.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/annotation.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/annotation.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/augment.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/augment.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/augment.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/augment.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/back_translating_alignment_emitter.cpp... 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Parsing file /build/reproducible-path/vg-1.59.0+ds/src/hts_alignment_emitter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/identity_overlay.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/identity_overlay.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/identity_overlay.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/identity_overlay.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/incremental_subgraph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/incremental_subgraph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/incremental_subgraph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/incremental_subgraph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/index_registry.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/index_registry.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/index_registry.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/index_registry.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/indexed_vg.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/indexed_vg.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/indexed_vg.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/indexed_vg.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/integrated_snarl_finder.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/integrated_snarl_finder.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/integrated_snarl_finder.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/integrated_snarl_finder.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/job_schedule.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/job_schedule.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/job_schedule.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/job_schedule.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/kff.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/kff.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/kff.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/kff.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/kmer.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/kmer.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/kmer.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/kmer.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/kmp.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/kmp.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/kmp.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/kmp.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/mapper.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/mapper.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/mapper.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/mapper.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/mcmc_caller.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/mcmc_caller.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/mcmc_caller.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/mcmc_caller.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/mcmc_genotyper.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/mcmc_genotyper.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/mcmc_genotyper.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/mcmc_genotyper.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/mem.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/mem.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/mem.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/mem.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/mem_accelerator.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/mem_accelerator.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/mem_accelerator.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/mem_accelerator.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/memoizing_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/memoizing_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/memoizing_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/memoizing_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/memusage.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/memusage.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/memusage.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/memusage.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/minimizer_mapper.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/minimizer_mapper.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/minimizer_mapper.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/minimizer_mapper.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/minimizer_mapper_from_chains.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/minimizer_mapper_from_chains.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/msa_converter.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/msa_converter.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/msa_converter.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/msa_converter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment_emitter.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment_emitter.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment_emitter.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment_emitter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/multipath_alignment_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/multipath_mapper.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/multipath_mapper.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/multipath_mapper.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/multipath_mapper.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/name_mapper.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/name_mapper.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/name_mapper.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/name_mapper.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/nested_traversal_finder.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/nested_traversal_finder.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/nested_traversal_finder.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/nested_traversal_finder.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/nodeside.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/nodeside.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/nodetraversal.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/nodetraversal.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/null_masking_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/null_masking_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/null_masking_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/null_masking_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/option.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/option.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/option.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/option.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/packer.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/packer.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/packer.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/packer.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/path.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/path.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/path.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/path.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/path_component_index.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/path_component_index.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/path_component_index.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/path_component_index.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/path_index.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/path_index.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/path_index.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/path_index.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/path_subgraph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/path_subgraph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/path_subgraph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/path_subgraph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/phase_unfolder.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/phase_unfolder.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/phase_unfolder.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/phase_unfolder.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/phased_genome.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/phased_genome.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/phased_genome.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/phased_genome.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/pictographs.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/pictographs.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/position.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/position.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/position.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/position.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/preflight.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/preflight.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/preflight.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/preflight.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/progressive.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/progressive.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/progressive.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/progressive.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/qual_adj_xdrop_aligner.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/qual_adj_xdrop_aligner.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/rare_variant_simplifier.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/rare_variant_simplifier.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/rare_variant_simplifier.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/rare_variant_simplifier.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/readfilter.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/readfilter.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/readfilter.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/readfilter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/recombinator.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/recombinator.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/recombinator.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/recombinator.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/region.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/region.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/region.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/region.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/region_expander.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/region_expander.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/region_expander.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/region_expander.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/reverse_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/reverse_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/reverse_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/reverse_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/sampler.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/sampler.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/sampler.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/sampler.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/scanner.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/scanner.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/scanner.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/scanner.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/sequence_complexity.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/sequence_complexity.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/small_bitset.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/small_bitset.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/small_snarl_simplifier.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/small_snarl_simplifier.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/small_snarl_simplifier.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/small_snarl_simplifier.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/snarl_caller.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/snarl_caller.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/snarl_caller.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/snarl_caller.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/snarl_distance_index.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/snarl_distance_index.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/snarl_distance_index.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/snarl_distance_index.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/snarl_seed_clusterer.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/snarl_seed_clusterer.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/snarl_seed_clusterer.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/snarl_seed_clusterer.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/snarls.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/snarls.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/snarls.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/snarls.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/source_sink_overlay.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/source_sink_overlay.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/source_sink_overlay.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/source_sink_overlay.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/sparse_union_find.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/sparse_union_find.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/sparse_union_find.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/sparse_union_find.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/splicing.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/splicing.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/splicing.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/splicing.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/split_strand_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/split_strand_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/split_strand_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/split_strand_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/ssw_aligner.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/ssw_aligner.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/ssw_aligner.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/ssw_aligner.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/statistics.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/statistics.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/statistics.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/statistics.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/stream_index.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/stream_index.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/stream_index.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/stream_index.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/stream_sorter.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/stream_sorter.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/stream_sorter.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/stream_sorter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subgraph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subgraph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subgraph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subgraph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subgraph_overlay.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subgraph_overlay.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subgraph_overlay.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subgraph_overlay.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subpath_overlay.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subpath_overlay.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subpath_overlay.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subpath_overlay.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/surjecting_alignment_emitter.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/surjecting_alignment_emitter.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/surjecting_alignment_emitter.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/surjecting_alignment_emitter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/surjector.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/surjector.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/surjector.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/surjector.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/swap_remove.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/swap_remove.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/transcriptome.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/transcriptome.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/transcriptome.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/transcriptome.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/translator.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/translator.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/translator.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/translator.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/traversal_clusters.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/traversal_clusters.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/traversal_clusters.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/traversal_clusters.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/traversal_finder.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/traversal_finder.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/traversal_finder.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/traversal_finder.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/traversal_support.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/traversal_support.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/traversal_support.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/traversal_support.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/tree_subgraph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/tree_subgraph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/tree_subgraph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/tree_subgraph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/types.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/types.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/utility.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/utility.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/utility.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/utility.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/variant_adder.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/variant_adder.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/variant_adder.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/variant_adder.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/variant_recall.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/variant_recall.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/variant_recall.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/variant_recall.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/vcf_buffer.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/vcf_buffer.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/vcf_buffer.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/vcf_buffer.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/vectorizer.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/vectorizer.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/vectorizer.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/vectorizer.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/version.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/version.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/version.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/version.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/vg.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/vg.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/vg.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/vg.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/vg_set.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/vg_set.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/vg_set.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/vg_set.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/viz.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/viz.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/viz.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/viz.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/wang_hash.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/wang_hash.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/watchdog.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/watchdog.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/watchdog.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/watchdog.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/xdrop_aligner.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/xdrop_aligner.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/zstdutil.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/zstdutil.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/zstdutil.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/zstdutil.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/a_star.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/a_star.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/alignment_path_offsets.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/alignment_path_offsets.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/alignment_path_offsets.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/alignment_path_offsets.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/approx_path_distance.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/approx_path_distance.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/approx_path_distance.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/approx_path_distance.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/back_translate.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/back_translate.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/back_translate.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/back_translate.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/chain_items.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/chain_items.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/chain_items.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/chain_items.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/component.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/component.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/component.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/component.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/count_covered.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/count_covered.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/coverage_depth.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/coverage_depth.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/coverage_depth.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/coverage_depth.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/dfs.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/dfs.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/dfs.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/dfs.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/disjoint_components.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/disjoint_components.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/disjoint_components.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/disjoint_components.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/distance_to_head.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/distance_to_head.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/distance_to_head.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/distance_to_head.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/distance_to_tail.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/distance_to_tail.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/distance_to_tail.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/distance_to_tail.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/expand_context.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/expand_context.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/expand_context.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/expand_context.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_connecting_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_connecting_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_connecting_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_connecting_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_containing_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_containing_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_containing_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_containing_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_extending_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_extending_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_extending_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/extract_extending_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_gbwt.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_gbwt.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_gbwt.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_gbwt.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_gbwtgraph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_gbwtgraph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_gbwtgraph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_gbwtgraph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_translation.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_translation.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_translation.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/find_translation.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/gfa_to_handle.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/gfa_to_handle.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/gfa_to_handle.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/gfa_to_handle.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/id_sort.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/id_sort.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/id_sort.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/id_sort.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/intersect_path_offsets.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/intersect_path_offsets.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/intersect_path_offsets.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/intersect_path_offsets.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/jump_along_path.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/jump_along_path.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/jump_along_path.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/jump_along_path.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/k_widest_paths.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/k_widest_paths.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/k_widest_paths.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/k_widest_paths.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/kmer.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/kmer.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/kmer.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/kmer.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/locally_expand_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/locally_expand_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/locally_expand_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/locally_expand_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/merge.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/merge.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/merge.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/merge.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/min_cut_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/min_cut_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/min_cut_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/min_cut_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/nearest_offsets_in_paths.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/nearest_offsets_in_paths.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/nearest_offsets_in_paths.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/nearest_offsets_in_paths.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/next_pos_chars.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/next_pos_chars.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/next_pos_chars.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/next_pos_chars.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/normalize.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/normalize.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/normalize.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/normalize.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/pad_band.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/pad_band.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/pad_band.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/pad_band.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/path_string.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/path_string.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/path_string.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/path_string.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/prune.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/prune.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/prune.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/prune.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/prune_to_connecting_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/prune_to_connecting_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/prune_to_connecting_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/prune_to_connecting_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/ref_path_distance.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/ref_path_distance.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/ref_path_distance.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/ref_path_distance.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/shortest_cycle.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/shortest_cycle.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/shortest_cycle.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/shortest_cycle.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/simplify_siblings.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/simplify_siblings.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/simplify_siblings.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/simplify_siblings.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/sorted_id_ranges.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/sorted_id_ranges.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/sorted_id_ranges.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/sorted_id_ranges.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/subgraph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/subgraph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/subgraph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/subgraph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/three_edge_connected_components.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/three_edge_connected_components.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/three_edge_connected_components.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/three_edge_connected_components.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/walk.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/walk.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/algorithms/walk.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/algorithms/walk.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/converted_hash_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/converted_hash_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/json_stream_helper.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/json_stream_helper.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/load_proto_to_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/load_proto_to_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/load_proto_to_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/load_proto_to_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_libvg_io.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_libvg_io.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_libvg_io.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_libvg_io.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_params_json.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_params_json.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_params_json.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_params_json.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_distance_index.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_distance_index.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_distance_index.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_distance_index.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbwt.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbwt.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbwt.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbwt.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbwtgraph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbwtgraph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbwtgraph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbwtgraph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbz.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbz.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbz.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbz.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbzgraph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbzgraph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbzgraph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gbzgraph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gcsa.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gcsa.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gcsa.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gcsa.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gfa.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gfa.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gfa.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_gfa.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_hash_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_hash_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_hash_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_hash_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_lcp.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_lcp.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_lcp.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_lcp.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_minimizer.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_minimizer.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_minimizer.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_minimizer.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_packed_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_packed_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_packed_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_packed_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_r_index.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_r_index.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_r_index.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_r_index.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_snarl_manager.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_snarl_manager.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_snarl_manager.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_snarl_manager.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_vg.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_vg.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_vg.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_vg.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_xg.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_xg.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_xg.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/register_loader_saver_xg.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/io/save_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/io/save_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/add_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/add_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/align_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/align_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/annotate_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/annotate_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/augment_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/augment_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/autoindex_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/autoindex_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/benchmark_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/benchmark_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/call_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/call_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/chain_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/chain_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/chunk_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/chunk_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/circularize_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/circularize_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/clip_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/clip_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/cluster_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/cluster_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/combine_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/combine_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/concat_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/concat_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/construct_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/construct_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/convert_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/convert_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/deconstruct_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/deconstruct_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/depth_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/depth_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/dotplot_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/dotplot_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/explode_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/explode_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/filter_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/filter_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/find_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/find_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/gamcompare_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/gamcompare_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/gampcompare_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/gampcompare_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/gamsort_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/gamsort_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/gbwt_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/gbwt_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/genotype_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/genotype_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/giraffe_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/giraffe_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/haplotypes_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/haplotypes_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/help_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/help_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/ids_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/ids_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/index_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/index_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/inject_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/inject_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/join_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/join_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/kmers_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/kmers_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/map_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/map_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/mcmc_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/mcmc_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/minimizer_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/minimizer_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/mod_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/mod_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/mpmap_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/mpmap_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/msga_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/msga_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/options.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/options.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/options.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/options.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/pack_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/pack_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/paths_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/paths_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/prune_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/prune_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/rna_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/rna_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/sift_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/sift_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/sim_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/sim_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/simplify_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/simplify_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/snarls_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/snarls_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/sort_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/sort_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/stats_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/stats_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/subcommand.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/subcommand.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/subcommand.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/subcommand.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/surject_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/surject_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/test_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/test_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/trace_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/trace_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/translate_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/translate_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/validate_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/validate_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/vectorize_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/vectorize_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/version_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/version_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/view_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/view_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/src/subcommand/viz_main.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/src/subcommand/viz_main.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/xg/src/xg.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/xg/src/xg.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/xg/src/xg.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/xg/src/xg.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/append_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/append_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/apply_orientations.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/apply_orientations.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/are_equivalent.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/are_equivalent.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/chop.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/chop.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/copy_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/copy_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/count_walks.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/count_walks.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dfs.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dfs.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dijkstra.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dijkstra.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/extend.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/extend.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_tips.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_tips.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/handle_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/handle_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_acyclic.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_acyclic.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_handle_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_handle_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_metadata.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_metadata.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_metadata.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_metadata.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/reverse_complement.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/reverse_complement.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/serializable.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/serializable.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/split_strands.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/split_strands.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/topological_sort.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/topological_sort.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/types.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/types.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/buildable_snarl_decomposition.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/buildable_snarl_decomposition.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/deletable_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/deletable_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/expanding_overlay_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/expanding_overlay_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_deletable_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_deletable_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_metadata.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_metadata.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_mutable_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_mutable_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/named_node_back_translation.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/named_node_back_translation.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/path_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/path_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/path_metadata.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/path_metadata.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/path_position_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/path_position_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/snarl_decomposition.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/snarl_decomposition.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/trivially_serializable.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/types.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/types.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/util.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/util.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_emitter.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_emitter.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_io.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_io.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/basic_stream.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/basic_stream.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/bin2ascii.h... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/bin2ascii.h... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/edit.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/edit.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/hfile_cppstream.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/hfile_cppstream.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/json2pb.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/json2pb.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_emitter.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_emitter.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_iterator.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_iterator.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/registry.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/registry.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream_multiplexer.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream_multiplexer.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/vpkg.cpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/vpkg.cpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/alignment_emitter.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/alignment_emitter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/alignment_io.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/alignment_io.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/basic_stream.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/blocked_gzip_input_stream.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/blocked_gzip_input_stream.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/blocked_gzip_output_stream.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/blocked_gzip_output_stream.hpp... Preprocessing /build/reproducibl/build/reproducible-path/vg-1.59.0+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-1.59.0+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-1.59.0+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-1.59.0+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-1.59.0+ds/deps/libhandlegraph/src/chop.cpp:2: warning: the name 'unchop.cpp' supplied as the argument in the \file statement is not an input file /build/reproducible-path/vg-1.59.0+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-1.59.0+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-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp:33: warning: Detected potential recursive class relation between class handlegraph::return_type_of and base class handlegraph::return_type_of< decltype(&std::remove_reference< Function >::type::operator())>! /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp:33: warning: Detected potential recursive class relation between class handlegraph::return_type_of and base class return_type_of< decltype(&std::remove_reference< Function >::type::operator())>! /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp:33: warning: Detected potential recursive class relation between class handlegraph::return_type_of and base class handlegraph::return_type_of< decltype(&std::remove_reference< Function >::type::operator())>! /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp:33: warning: Detected potential recursive class relation between class handlegraph::return_type_of and base class return_type_of< decltype(&std::remove_reference< Function >::type::operator())>! /build/reproducible-path/vg-1.59.0+ds/src/alignment.hpp:307: warning: no matching file member found for void vg::parse_bed_regions(std::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 1901 of file /build/reproducible-path/vg-1.59.0+ds/src/alignment.cpp 'void parse_bed_regions(istream &bedstream, const PathPositionHandleGraph *graph, const std::function< void(Alignment &)> &callback)' at line 1910 of file /build/reproducible-path/vg-1.59.0+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-1.59.0+ds/src/region.cpp /build/reproducible-path/vg-1.59.0+ds/src/alignment.hpp:310: 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 2179 of file /build/reproducible-path/vg-1.59.0+ds/src/alignment.cpp 'void parse_gff_regions(istream &gffstream, const PathPositionHandleGraph *graph, const std::function< void(Alignment &)> &callback)' at line 2188 of file /build/reproducible-path/vg-1.59.0+ds/src/alignment.cpp /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/registry.hpp:67: 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-1.59.0+ds/deps/libvgio/src/registry.cpp e-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/edit.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/edit.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/fdstream.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/fdstream.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/gafkluge.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/hfile_cppstream.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/hfile_cppstream.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/hfile_internal.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/hfile_internal.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/json2pb.h... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/json2pb.h... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/loader.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/loader.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/message_emitter.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/message_emitter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/message_iterator.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/protobuf_emitter.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/protobuf_emitter.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/registry.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/registry.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/stream.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/stream.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/stream_multiplexer.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/stream_multiplexer.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/vpkg.hpp... Parsing file /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/vpkg.hpp... Preprocessing /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto... Parsing file /build/reproducible-path/vg-1.59.0+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... Building concept list... Computing nesting relations for classes... Associating documentation with classes... Associating documentation with concepts... Associating documentation with modules... 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... Computing module relations... 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/chop.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_metadata.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/named_node_back_translation.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/path_handle_graph.hpp... Generating docs for file deps/libhandlegraph/src/include/handlegraph/path_metadata.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/mutable_path_handle_graph.cpp... Generating docs for file deps/libhandlegraph/src/mutable_path_metadata.cpp... Generating docs for file deps/libhandlegraph/src/path_handle_graph.cpp... Generating docs for file deps/libhandlegraph/src/path_metadata.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/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/back_translate.cpp... Generating docs for file src/algorithms/back_translate.hpp... Generating docs for file src/algorithms/chain_items.cpp... Generating docs for file src/algorithms/chain_items.hpp... Generating docs for file src/algorithms/component.cpp... Generating docs for file src/algorithms/component.hpp... Generating docs for file src/algorithms/count_covered.hpp... Generating docs for file src/algorithms/coverage_depth.cpp... Generating docs for file src/algorithms/coverage_depth.hpp... Generating docs for file deps/libhandlegraph/src/dfs.cpp... 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/find_gbwt.cpp... Generating docs for file src/algorithms/find_gbwt.hpp... Generating docs for file src/algorithms/find_gbwtgraph.cpp... Generating docs for file src/algorithms/find_gbwtgraph.hpp... Generating docs for file src/algorithms/find_translation.cpp... Generating docs for file src/algorithms/find_translation.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/intersect_path_offsets.cpp... Generating docs for file src/algorithms/intersect_path_offsets.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/locally_expand_graph.cpp... Generating docs for file src/algorithms/locally_expand_graph.hpp... Generating docs for file src/algorithms/merge.cpp... Generating docs for file src/algorithms/merge.hpp... Generating docs for file src/algorithms/min_cut_graph.cpp... Generating docs for file src/algorithms/min_cut_graph.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/pad_band.cpp... Generating docs for file src/algorithms/pad_band.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/prune_to_connecting_graph.cpp... Generating docs for file src/algorithms/prune_to_connecting_graph.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/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/back_translating_alignment_emitter.cpp... Generating docs for file src/back_translating_alignment_emitter.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/clip.cpp... Generating docs for file src/clip.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/contracting_graph.cpp... Generating docs for file src/contracting_graph.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/explainer.cpp... Generating docs for file src/explainer.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/flat_file_back_translation.cpp... 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Generating docs for compound vg::edit_t... Generating docs for compound vg::EditedTranscriptPath... Generating docs for compound vg::endianness... Generating docs for compound vg::ExhaustiveTraversalFinder... Generating docs for compound vg::Exon... Generating docs for compound vg::Explainer... 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::FixedGenotypePriorCalculator... Generating docs for compound vg::FlatFileBackTranslation... Generating docs for compound vg::FlowCaller... 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::FlowTraversalFinder... Generating docs for compound vg::FragmentLengthDistribution... Generating docs for compound vg::FragmentLengthStatistics... 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::PaintableSpace... Generating docs for nested compound vg::Funnel::Stage... Generating docs for compound vg::GAFOutputCaller... Generating docs for compound vg::GaplessExtender... Generating docs for compound vg::GaplessExtension... Generating docs for compound vg::GBWTHandler... Generating docs for compound vg::GBWTTraversalFinder... Generating docs for compound vg::GBZGraph... Generating docs for compound vg::GenomeState... Generating docs for compound vg::GenomeStateCommand... Generating docs for compound vg::Genotype... Generating docs for compound vg::GenotypeLikelihoodCalculator... Generating docs for compound vg::GenotypePriorCalculator... 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::GFAHandleGraph... Generating docs for compound vg::GFFReader... Generating docs for compound vg::GFFRecord... Generating docs for compound vg::Graph... Generating docs for compound vg::GraphCaller... Generating docs for compound vg::GraphSynchronizer... Generating docs for nested compound vg::GraphSynchronizer::Lock... Generating docs for compound vg::GreedyMinDistanceClusterer... Generating docs for compound vg::GSSWAligner... Generating docs for compound vg::HandleGraphNodeSet... Generating docs for compound vg::HandleGraphSnarlFinder... Generating docs for compound vg::HaplotypeIndexer... Generating docs for compound vg::HaplotypePartitioner... Generating docs for nested compound vg::HaplotypePartitioner::Parameters... Generating docs for nested compound vg::HaplotypePartitioner::Subchain... Generating docs for compound vg::Haplotypes... Generating docs for nested compound vg::Haplotypes::Header... Generating docs for nested compound vg::Haplotypes::Subchain... Generating docs for nested compound vg::Haplotypes::TopLevelChain... Generating docs for compound vg::hash_map... Generating docs for compound vg::hash_map< K *, V >... Generating docs for compound vg::hash_set... Generating docs for compound vg::hash_set< K * >... Generating docs for compound vg::HTSAlignmentEmitter... Generating docs for compound vg::HTSWriter... Generating docs for compound vg::IdentityOverlay... Generating docs for compound vg::IDScanner... Generating docs for compound vg::IncrementalSubgraph... Generating docs for nested compound vg::IncrementalSubgraph::FCmp... Generating docs for nested compound vg::IncrementalSubgraph::IterFCmp... Generating docs for compound vg::IncrementIter... Generating docs for compound vg::IndexedVG... Generating docs for nested compound vg::IndexedVG::CacheEntry... Generating docs for compound vg::IndexFile... Generating docs for compound vg::IndexingParameters... Generating docs for compound vg::IndexingPlan... Generating docs for compound vg::IndexRecipe... Generating docs for compound vg::IndexRegistry... Generating docs for compound vg::InsertHaplotypeCommand... Generating docs for compound vg::InsufficientInputException... Generating docs for compound vg::IntegratedSnarlFinder... Generating docs for nested compound vg::IntegratedSnarlFinder::MergedAdjacencyGraph... Generating docs for compound vg::is_instantiation_of... Generating docs for compound vg::is_instantiation_of< Predicate< PredicateArgs... >, Predicate >... Generating docs for compound vg::JobSchedule... Generating docs for compound vg::JoinedSpliceGraph... Generating docs for compound vg::kff_recoding_t... Generating docs for compound vg::kmer_t... Generating docs for compound vg::KmerMatch... Generating docs for compound vg::KmerPosition... Generating docs for compound vg::LazyRNG... Generating docs for compound vg::LegacyCaller... Generating docs for compound vg::LocationSupport... Generating docs for compound vg::Locus... Generating docs for compound vg::Mapper... Generating docs for compound vg::Mapping... Generating docs for compound vg::mapping_t... Generating docs for compound vg::MappingHash... Generating docs for compound vg::MatchPos... Generating docs for nested compound vg::MatchPos::PathList... Generating docs for compound vg::MaximalExactMatch... Generating docs for compound vg::MCMCCaller... Generating docs for compound vg::MCMCGenotyper... Generating docs for compound vg::MEMAccelerator... Generating docs for compound vg::MEMChainModel... Generating docs for compound vg::MEMChainModelVertex... 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::MemoizingGraph... Generating docs for compound vg::MinDistanceClusterer... Generating docs for compound vg::MinimizerMapper... Generating docs for nested compound vg::MinimizerMapper::Minimizer... Generating docs for compound vg::MIPayload... Generating docs for compound vg::MIPayloadValues... Generating docs for compound vg::MSAConverter... Generating docs for compound vg::multipath_alignment_t... Generating docs for compound vg::MultipathAlignment... Generating docs for compound vg::MultipathAlignmentEmitter... Generating docs for compound vg::MultipathAlignmentGraph... Generating docs for compound vg::MultipathMapper... Generating docs for compound vg::MultipathProblem... Generating docs for compound vg::NameMapper... Generating docs for compound vg::NestedCachedPackedTraversalSupportFinder... Generating docs for nested compound vg::NestedCachedPackedTraversalSupportFinder::snarl_less... Generating docs for compound vg::NestedFlowCaller... Generating docs for nested compound vg::NestedFlowCaller::CallRecord... Generating docs for compound vg::NestedTraversalFinder... Generating docs for compound vg::NetGraph... Generating docs for compound vg::NGSSimulator... Generating docs for nested compound vg::NGSSimulator::MarkovDistribution... Generating docs for compound vg::NoAlignmentInBandException... Generating docs for compound vg::Node... Generating docs for compound vg::NodePileup... Generating docs for compound vg::NodeSide... Generating docs for compound vg::NodeTraversal... Generating docs for compound vg::normal_distribution... Generating docs for compound vg::NullClusterer... Generating docs for compound vg::NullMaskingGraph... Generating docs for compound vg::Option... Generating docs for compound vg::Option< vector< Item /build/reproducible-path/vg-1.59.0+ds/src/packer.hpp:61: warning: Unsupported xml/html tag found >, Parser >... Generating docs for compound vg::OptionInterface... Generating docs for compound vg::OptionValueParser... Generating docs for compound vg::OptionValueParser< vector< Item > >... Generating docs for compound vg::OrientedDistanceClusterer... Generating docs for compound vg::OrientedDistanceMeasurer... Generating docs for compound vg::PackedTraversalSupportFinder... Generating docs for compound vg::Packer... Generating docs for compound vg::Packers... Generating docs for compound vg::pair_hash_map... Generating docs for compound vg::pair_hash_set... Generating docs for compound vg::PairedEndMapper... Generating docs for compound vg::ParallelKFFReader... Generating docs for compound vg::ParentGenotypeInfo... Generating docs for compound vg::Path... Generating docs for compound vg::path_mapping_t... Generating docs for compound vg::path_t... Generating docs for compound vg::PathBasedTraversalFinder... Generating docs for compound vg::PathBranch... Generating docs for compound vg::PathChunker... Generating docs for compound vg::PathComponentIndex... Generating docs for compound vg::PathIndex... Generating docs for compound vg::PathNode... Generating docs for compound vg::PathOrientedDistanceMeasurer... Generating docs for compound vg::PathRestrictedTraversalFinder... Generating docs for compound vg::Paths... Generating docs for compound vg::PathSubgraph... Generating docs for compound vg::PathSubgraphOverlay... Generating docs for compound vg::PathTraversalFinder... 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::PhaseUnfolder... Generating docs for compound vg::Pictographs... Generating docs for compound vg::Pileup... Generating docs for compound vg::PoissonSupportSnarlCaller... Generating docs for nested compound vg::PoissonSupportSnarlCaller::PoissonCallInfo... Generating docs for compound vg::Position... Generating docs for compound vg::position_t... Generating docs for compound vg::PositionIDScanner... Generating docs for compound vg::ProblemDumpExplainer... Generating docs for compound vg::Progressive... Generating docs for compound vg::QualAdjAligner... Generating docs for compound vg::QualAdjXdropAligner... Generating docs for compound vg::Range... Generating docs for compound vg::RareVariantSimplifier... Generating docs for compound vg::RatioSupportSnarlCaller... Generating docs for compound vg::read_alignment_index_t... Generating docs for compound vg::ReadFilter... Generating docs for compound vg::ReadMasker... Generating docs for compound vg::ReadRestrictedTraversalFinder... Generating docs for compound vg::RebuildJob... Generating docs for compound vg::RebuildParameters... Generating docs for compound vg::Recombinator... Generating docs for nested compound vg::Recombinator::LocalHaplotype... Generating docs for nested compound vg::Recombinator::Parameters... Generating docs for nested compound vg::Recombinator::Statistics... Generating docs for compound vg::RecombinatorHaplotype... Generating docs for compound vg::Region... Generating docs for compound vg::RegionExpander... Generating docs for compound vg::ReplaceLocalHaplotypeCommand... Generating docs for compound vg::ReplaceSnarlHaplotypeCommand... Generating docs for compound vg::RepresentativeTraversalFinder... Generating docs for compound vg::ReverseGraph... Generating docs for compound vg::RewindPlanException... Generating docs for compound vg::Sampler... Generating docs for compound vg::SeqComplexity... Generating docs for compound vg::ShuffledPairs... Generating docs for nested compound vg::ShuffledPairs::iterator... Generating docs for compound vg::SimpleConsistencyCalculator... Generating docs for compound vg::SimpleTraversalSupportCalculator... Generating docs for compound vg::SizeLimitExceededException... Generating docs for compound vg::SmallBitset... Generating docs for compound vg::SmallSnarlSimplifi/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto:268: warning: Unsupported xml/html tag found /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto:268: warning: Unsupported xml/html tag found er... Generating docs for compound vg::Snarl... Generating docs for compound vg::SnarlCaller... Generating docs for nested compound vg::SnarlCaller::CallInfo... Generating docs for compound vg::SnarlDistanceIndexClusterer... Generating docs for nested compound vg::SnarlDistanceIndexClusterer::Cluster... Generating docs for nested compound vg::SnarlDistanceIndexClusterer::ClusterHead... Generating docs for nested compound vg::SnarlDistanceIndexClusterer::ClusteringProblem... Generating docs for nested compound vg::SnarlDistanceIndexClusterer::Seed... Generating docs for nested compound vg::SnarlDistanceIndexClusterer::SeedCache... Generating docs for nested compound vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem... Generating docs for nested compound vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild... Generating docs for compound vg::SnarlFinder... Generating docs for compound vg::SnarlGraph... Generating docs for compound vg::SnarlManager... Generating docs for nested compound vg::SnarlManager::SnarlRecord... Generating docs for compound vg::SnarlMinDistance... Generating docs for compound vg::SnarlOrientedDistanceMeasurer... Generating docs for compound vg::SnarlState... Generating docs for compound vg::SnarlTraversal... Generating docs for compound vg::SourceSinkOverlay... Generating docs for compound vg::SparseUnionFind... Generating docs for compound vg::SplicedHTSAlignmentEmitter... Generating docs for compound vg::SpliceRegion... Generating docs for compound vg::SpliceStats... Generating docs for compound vg::SSWAligner... Generating docs for compound vg::state_hash... Generating docs for compound vg::StrandSplitGraph... Generating docs for compound vg::StreamIndex... Generating docs for compound vg::StreamIndexBase... Generating docs for compound vg::StreamSorter... Generating docs for compound vg::string_hash_map... Generating docs for compound vg::string_hash_set... Generating docs for compound vg::SubgraphOverlay... Generating docs for compound vg::SubHandleGraph... Generating docs for compound vg::Subpath... Generating docs for compound vg::subpath_t... Generating docs for compound vg::SubpathOverlay... Generating docs for compound vg::SummaryStatistics... Generating docs for compound vg::Support... Generating docs for compound vg::SupportAugmentedGraph... Generating docs for compound vg::SupportBasedSnarlCaller... Generating docs for compound vg::SupportRestrictedTraversalFinder... Generating docs for compound vg::SurjectingAlignmentEmitter... Generating docs for compound vg::Surjector... Generating docs for compound vg::SwapHaplotypesCommand... Generating docs for compound vg::TargetValueSearch... Generating docs for compound vg::TipAnchoredMaxDistance... Generating docs for compound vg::Transcript... Generating docs for compound vg::Transcriptome... Generating docs for compound vg::TranscriptPath... Generating docs for compound vg::Translation... Generating docs for compound vg::Translator... Generating docs for compound vg::TraversalFinder... Generating docs for compound vg::TraversalSupportCalculator... Generating docs for compound vg::TraversalSupportFinder... Generating docs for compound vg::Tree... Generating docs for compound vg::TreeNode... Generating docs for compound vg::TreeSubgraph... Generating docs for compound vg::TrivialTraversalFinder... Generating docs for compound vg::truncated_normal_distribution... Generating docs for compound vg::TVSClusterer... Generating docs for compound vg::uniform_int_distribution... Generating docs for compound vg::uniform_real_distribution... Generating docs for compound vg::VariantAdder... Generating docs for compound vg::VcfBuffer... Generating docs for compound vg::VCFGenotyper... Generating docs for compound vg::VCFOutputCaller... Generating docs for compound vg::VcfRecordConverter... Generating docs for compound vg::VcfRecordFilter... Generating docs for compound vg::VCFTraversalFinder... Generating docs for compound vg::VectorView... Generating docs for nested compound vg::VectorView::const_iterator... Generating docs for compoun/build/reproducible-path/vg-1.59.0+ds/src/vg.hpp:881: warning: explicit link request to 'matches' could not be resolved /build/reproducible-path/vg-1.59.0+ds/src/vg.hpp:881: warning: explicit link request to 'mismatches' could not be resolved d vg::VectorViewInverse... Generating docs for compound vg::Version... Generating docs for compound vg::VG... Generating docs for nested compound vg::VG::Plan... Generating docs for compound vg::VGIndexes... Generating docs for compound vg::VGset... Generating docs for compound vg::Visit... Generating docs for compound vg::Viz... Generating docs for compound vg::wang_hash... Generating docs for compound vg::wang_hash< handle_t >... Generating docs for compound vg::wang_hash< handlegraph::net_handle_t >... Generating docs for compound vg::wang_hash< NodeSide >... Generating docs for compound vg::wang_hash< NodeTraversal >... Generating docs for compound vg::wang_hash< path_handle_t >... Generating docs for compound vg::wang_hash< std::pair< A, B > >... 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::Watchdog... Generating docs for nested compound vg::Watchdog::thread_state_t... Generating docs for compound vg::WFAAlignment... Generating docs for compound vg::WFAExtender... Generating docs for nested compound vg::WFAExtender::ErrorModel... Generating docs for nested compound vg::WFAExtender::ErrorModel::Event... Generating docs for compound vg::WFANode... Generating docs for compound vg::WFAPoint... Generating docs for compound vg::WFATree... Generating docs for nested compound vg::WFATree::ScoreProperties... Generating docs for compound vg::WideningPRNG... Generating docs for compound vg::WindowedVcfBuffer... Generating docs for compound vg::WrappingPositionScanner... Generating docs for compound vg::XdropAligner... Generating docs for namespace vg::algorithms Generating docs for compound vg::algorithms::Anchor... Generating docs for compound vg::algorithms::Edge... Generating docs for compound vg::algorithms::GFADuplicatePathError... Generating docs for compound vg::algorithms::GFAFormatError... Generating docs for compound vg::algorithms::GFAIDMapInfo... Generating docs for compound vg::algorithms::GFAParser... Generating docs for compound vg::algorithms::Graph... Generating docs for compound vg::algorithms::kmer_t... Generating docs for compound vg::algorithms::Node... Generating docs for compound vg::algorithms::TracedScore... Generating docs for compound vg::algorithms::walk_t... Generating docs for namespace vg::io Generating docs for compound vg::io::AlignmentEmitter... Generating docs for compound vg::io::BlockedGzipInputStream... Generating docs for compound vg::io::BlockedGzipOutputStream... Generating docs for compound vg::io::ConvertedHashGraph... Generating docs for compound vg::io::fdinbuf... Generating docs for compound vg::io::fdistream... Generating docs for compound vg::io::fdostream... Generating docs for compound vg::io::fdoutbuf... Generating docs for compound vg::io::GafAlignmentEmitter... Generating docs for compound vg::io::hFILE_cppstream... Generating docs for compound vg::io::JSONStreamHelper... Generating docs for compound vg::io::MessageEmitter... Generating docs for compound vg::io::MessageIterator... Generating docs for compound vg::io::NullAlignmentEmitter... 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::streaminbuf... Generating docs for compound vg::io::streamistream... Generating docs for compound vg::io::StreamMultiplexer... Generating docs for compound vg::io::TSVAlignmentEmitter... Generating docs for compound vg::io::VGAlignmentEmitter... Generating docs for compound vg::io::VPKG... Generating docs for namespace vg::subcommand Generating docs for compound vg::subcommand::ArgSpec... Generating docs for compound vg::subcommand::BaseArgSpec... Generating docs for compound vg::subcommand::BaseOptionGroup... Generating docs for compound vg::subcommand::BaseValuation... Generating docs for compound vg::subcommand::FlagArgSpec../build/reproducible-path/vg-1.59.0+ds/src/banded_global_aligner.hpp:88: warning: Unsupported xml/html tag found . Generating docs for compound vg::subcommand::GroupedOptionGroup... Generating docs for compound vg::subcommand::OptionGroup... Generating docs for compound vg::subcommand::Preset... Generating docs for compound vg::subcommand::RangeArgSpec... Generating docs for compound vg::subcommand::Subcommand... Generating docs for compound vg::subcommand::TickChainLink... Generating docs for compound vg::subcommand::Valuation... Generating docs for compound vg::subcommand::ValueArgSpec... Generating docs for namespace vg::temp_file Generating docs for compound vg::temp_file::Handler... Generating docs for namespace xg Generating docs for compound xg::XG... Generating docs for compound xg::XGFormatError... Generating docs for compound xg::XGPath... Generating docs for namespace xg::temp_file Generating docs for compound xg::temp_file::Handler... Generating docs for namespace zstdutil Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating topic index... Generating module index... Generating module member index... Generating namespace index... Generating namespace member index... Generating concept 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::AbstractReadSampler Generating XML output for class vg::Genotyper::Affinity Generating XML output for class vg::AliasGraph 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::alignment_index_t 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::AlignmentValidity Generating XML output for class vg::BandedGlobalAligner::AltTracebackStack Generating XML output for class vg::algorithms::Anchor Generating XML output for class vg::Annotation Generating XML output for class vg::AppendHaplotypeCommand Generating XML output for class vg::subcommand::ArgSpec Generating XML output for class vg::AugmentedGraph Generating XML output for class vg::BandedGlobalAligner::BABuilder Generating XML output for class vg::BackTranslatingAlignmentEmitter 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::subcommand::BaseArgSpec Generating XML output for class vg::BaseMapper Generating XML output for class vg::BaseOption Generating XML output for class vg::subcommand::BaseOptionGroup Generating XML output for class vg::BasePileup Generating XML output for class vg::subcommand::BaseValuation Generating XML output for class vg::BBEdgeHash 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, false > Generating XML output for class handlegraph::BoolReturningWrapper< Iteratee, true > 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::NestedFlowCaller::CallRecord Generating XML outp/build/reproducible-path/vg-1.59.0+ds/src/filter.cpp:939: warning: Unsupported xml/html tag found ut for class vg::ChainIterator Generating XML output for class vg::SnarlDistanceIndexClusterer::Cluster Generating XML output for class vg::SnarlDistanceIndexClusterer::ClusterHead Generating XML output for class vg::SnarlDistanceIndexClusterer::ClusteringProblem Generating XML output for class vg::Colors Generating XML output for class compare_gaf 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::VectorView::const_iterator Generating XML output for class vg::ConstructedChunk Generating XML output for class vg::Constructor Generating XML output for class vg::ContractingGraph Generating XML output for class vg::io::ConvertedHashGraph Generating XML output for class vg::count_back_inserter 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::DiagramExplainer 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::DotDumpExplainer Generating XML output for class vg::DozeuInterface Generating XML output for class vg::DozeuPinningOverlay Generating XML output for class vg::MEMClusterer::DPScoreComparator Generating XML output for class vg::algorithms::Edge 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::WFAExtender::ErrorModel Generating XML output for class vg::WFAExtender::ErrorModel::Event 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::Explainer Generating XML output for class vg::ExtraNodeGraph Generating XML output for class vg::IncrementalSubgraph::FCmp 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::subcommand::FlagArgSpec Generating XML output for class vg::FlatFileBackTranslation 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 GafFile 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 GBWTConfig 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::GBZGraph 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::GFADuplicatePathError Generating XML output for class vg::algorithms::GFAFormatError Generating XML output for class vg::GFAHandleGraph Generating XML output for class vg::algorithms::GFAIDMapInfo Generating XML output for class vg::algorithms::GFAParser Generating XML output for class vg::GFFReader Generating XML output for class vg::GFFRecord Generating XML output for class GiraffeMainOptions Generating XML output for class vg::algorithms::Graph 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 GraphHandler Generating XML output for class vg::GraphSynchronizer Generating XML output for class greater_gaffile Generating XML output for class vg::GreedyMinDistanceClusterer Generating XML output for class vg::subcommand::GroupedOptionGroup 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::HandleGraphNodeSet 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 vg::HaplotypePartitioner Generating XML output for class vg::Haplotypes Generating XML output for class HaplotypesConfig 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 vg::Haplotypes::Header 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::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::IndexingPlan 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 vg::IncrementalSubgraph::IterFCmp Generating XML output for class j2pb_error Generating XML output for class job_type Generating XML output for class vg::JobSchedule 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::kff_recoding_t 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::LazyRNG 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::Recombinator::LocalHaplotype 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::MappingHash Generating XML output for class MappingRun Generating XML output for class vg::NGSSimulator::MarkovDistribution Generating XML output for class vg::MatchPos 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::MEMAccelerator 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::MIPayload Generating XML output for class vg::MIPayloadValues 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::MutablePathMetadata Generating XML output for class handlegraph::MutablePathMutableHandleGraph Generating XML o/build/reproducible-path/vg-1.59.0+ds/src/packer.hpp:61: warning: Unsupported xml/html tag found utput for class handlegraph::NamedNodeBackTranslation Generating XML output for class vg::NameMapper Generating XML output for class vg::NestedCachedPackedTraversalSupportFinder Generating XML output for class vg::NestedFlowCaller Generating XML output for class vg::NestedTraversalFinder Generating XML output for class vg::Deconstructor::NestingInfo Generating XML output for class handlegraph::net_handle_t Generating XML output for class vg::NetGraph Generating XML output for class vg::NGSSimulator Generating XML output for class vg::NoAlignmentInBandException Generating XML output for class vg::algorithms::Node Generating XML output for class vg::Node 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::subcommand::OptionGroup 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::Funnel::PaintableSpace 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::ParallelKFFReader Generating XML output for class vg::HaplotypePartitioner::Parameters Generating XML output for class vg::Recombinator::Parameters Generating XML output for class vg::ParentGenotypeInfo 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::MatchPos::PathList Generating XML output for class handlegraph::PathMetadata 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::subcommand::Preset Generating XML output for class vg::ProblemDumpExplainer Generating XML output for class vg::Progressive Generating XML output for class vg::io::ProtobufEm/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto:268: warning: Unsupported xml/html tag found /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto:268: warning: Unsupported xml/html tag found itter 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 vg::subcommand::RangeArgSpec Generating XML output for class handlegraph::RankedHandleGraph Generating XML output for class vg::RareVariantSimplifier Generating XML output for class vg::RatioSupportSnarlCaller Generating XML output for class vg::read_alignment_index_t Generating XML output for class vg::ReadFilter Generating XML output for class vg::ReadMasker Generating XML output for class vg::ReadRestrictedTraversalFinder Generating XML output for class vg::RebuildJob Generating XML output for class vg::RebuildParameters Generating XML output for class vg::Recombinator Generating XML output for class vg::RecombinatorHaplotype Generating XML output for class ReferenceInterval 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 handlegraph::return_type_of Generating XML output for class handlegraph::return_type_of< Returns(*)(Args...)> Generating XML output for class handlegraph::return_type_of< Returns(Owner::*)(Args...) const > Generating XML output for class handlegraph::return_type_of< Returns(Owner::*)(Args...)> Generating XML output for class vg::ReverseGraph Generating XML output for class vg::RewindPlanException Generating XML output for class haplo::haploMath::RRMemo Generating XML output for class vg::Sampler Generating XML output for class vg::WFATree::ScoreProperties Generating XML output for class haplo::ScoreProvider Generating XML output for class ScoringOptions Generating XML output for class vg::SnarlDistanceIndexClusterer::Seed Generating XML output for class vg::SnarlDistanceIndexClusterer::SeedCache 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::SizeLimitExceededException 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::NestedCachedPackedTraversalSupportFinder::snarl_less Generating XML output for class vg::SnarlCaller Generating XML output for class handlegraph::SnarlDecomposition Generating XML output for class vg::SnarlDistanceIndexClusterer Generating XML output for class vg::SnarlFinder Generating XML output for class vg::SnarlGraph 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::SnarlState Generating XML output for class vg::SnarlTraversal Generating XML output for class vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild Generating XML output for class vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem Generating XML output for class haplo::linear_haplo_structure::SNVvector Generating XML output for class vg::SourceSinkOverlay Generating XML output for class vg::SparseUnionFind Generating XML output for class vg::SplicedHTSAlignmentEmitter Generating XML output for class vg::SpliceRegion Generating XML output for class vg::SpliceStats Generating XML output for class vg::SSWAligner Generating XML output for class vg::Funnel::Stage Generating XML output for class vg::state_hash Generati/build/reproducible-path/vg-1.59.0+ds/src/vg.hpp:881: warning: explicit link request to 'matches' could not be resolved /build/reproducible-path/vg-1.59.0+ds/src/vg.hpp:881: warning: explicit link request to 'mismatches' could not be resolved ng XML output for class vg::Recombinator::Statistics 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::HaplotypePartitioner::Subchain Generating XML output for class vg::Haplotypes::Subchain 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::SubpathOverlay Generating XML output for class vg::SummaryStatistics 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::subcommand::TickChainLink Generating XML output for class vg::TipAnchoredMaxDistance Generating XML output for class vg::Haplotypes::TopLevelChain Generating XML output for class vg::algorithms::TracedScore 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::Translation 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::TreeSubgraph Generating XML output for class handlegraph::TriviallySerializable Generating XML output for class vg::TrivialTraversalFinder Generating XML output for class vg::truncated_normal_distribution 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::subcommand::Valuation Generating XML output for class vg::subcommand::ValueArgSpec 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::VectorView Generating XML output for class vg::VectorViewInverse 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/build/reproducible-path/vg-1.59.0+ds/src/hts_alignment_emitter.hpp:68: warning: Found unknown command '@SQ' 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< handlegraph::net_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::WFAAlignment Generating XML output for class vg::WFAExtender Generating XML output for class vg::WFANode Generating XML output for class vg::WFAPoint Generating XML output for class vg::WFATree 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 @515 Generating XML output for namespace bdsg Generating XML output for namespace gafkluge 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 handlegraph::algorithms::internal 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::@94 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 xg Generating XML output for namespace xg::temp_file Generating XML output for namespace zstdutil 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 chop.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_metadata.hpp Generating XML output for file mutable_path_mutable_handle_graph.hpp Generating XML output for file named_node_back_translation.hpp Generating XML output for file path_handle_graph.hpp Generating XML output for file path_metadata.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 mutable_path_handle_graph.cpp Generating XML output for file mutable_path_metadata.cpp Generating XML output for file path_handle_graph.cpp Generating XML output for file path_metadata.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 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 back_translate.cpp Generating XML output for file back_translate.hpp Generating XML output for file chain_items.cpp Generating XML output for file chain_items.hpp Generating XML output for file component.cpp Generating XML output for file component.hpp Generating XML output for file count_covered.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.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 find_gbwt.cpp Generating XML output for file find_gbwt.hpp Generating XML output for file find_gbwtgraph.cpp Generating XML output for file find_gbwtgraph.hpp Generating XML output for file find_translation.cpp Generating XML output for file find_translation.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 intersect_path_offsets.cpp Generating XML output for file intersect_path_offsets.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 locally_expand_graph.cpp Generating XML output for file locally_expand_graph.hpp Generating XML output for file merge.cpp Generating XML output for file merge.hpp Generating XML output for file min_cut_graph.cpp Generating XML output for file min_cut_graph.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 pad_band.cpp Generating XML output for file pad_band.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 prune_to_connecting_graph.cpp Generating XML output for file prune_to_connecting_graph.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 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 back_translating_alignment_emitter.cpp Generating XML output for file back_translating_alignment_emitter.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 clip.cpp Generating XML output for file clip.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 contracting_graph.cpp Generating XML output for file contracting_graph.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 explainer.cpp Generating XML output for file explainer.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 flat_file_back_translation.cpp Generating XML output for file flat_file_back_translation.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 gbwt_extender.cpp Generating XML output for file gbwt_extender.hpp Generating XML output for file gbwt_helper.cpp Generating XML output for file gbwt_helper.hpp Generating XML output for file gbwtgraph_helper.cpp Generating XML output for file gbwtgraph_helper.hpp Generating XML output for file gbzgraph.hpp Generating XML output for file gcsa_helper.cpp Generating XML output for file gcsa_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 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_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_params_json.cpp Generating XML output for file register_loader_params_json.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_gbz.cpp Generating XML output for file register_loader_saver_gbz.hpp Generating XML output for file register_loader_saver_gbzgraph.cpp Generating XML output for file register_loader_saver_gbzgraph.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_gfa.cpp Generating XML output for file register_loader_saver_gfa.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_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 job_schedule.cpp Generating XML output for file job_schedule.hpp Generating XML output for file kff.cpp Generating XML output for file kff.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 kmp.cpp Generating XML output for file kmp.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 mem_accelerator.cpp Generating XML output for file mem_accelerator.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 minimizer_mapper.cpp Generating XML output for file minimizer_mapper.hpp Generating XML output for file minimizer_mapper_from_chains.cpp 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 recombinator.cpp Generating XML output for file recombinator.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 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 snarl_distance_index.cpp Generating XML output for file snarl_distance_index.hpp Generating XML output for file snarl_seed_clusterer.cpp Generating XML output for file snarl_seed_clusterer.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 sparse_union_find.cpp Generating XML output for file sparse_union_find.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 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 chain_main.cpp Generating XML output for file chunk_main.cpp Generating XML output for file circularize_main.cpp Generating XML output for file clip_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 haplotypes_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 options.cpp Generating XML output for file options.hpp 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 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 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 subpath_overlay.cpp Generating XML output for file subpath_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_clusters.cpp Generating XML output for file traversal_clusters.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 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 Generating XML output for file zstdutil.cpp Generating XML output for file zstdutil.hpp Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/src/algorithms/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/handlegraph/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/io/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/src/io/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/xg/src/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/src/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/src/subcommand/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include/vg/ Generate XML output for dir /build/reproducible-path/vg-1.59.0+ds/deps/xg/ Running plantuml with JAVA... type lookup cache used 14490/65536 hits=97426 misses=16651 symbol lookup cache used 11222/65536 hits=148517 misses=11222 finished... echo "View documentation at: file:///build/reproducible-path/vg-1.59.0+ds/doc/doxygen/index.html" View documentation at: file:///build/reproducible-path/vg-1.59.0+ds/doc/doxygen/index.html make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' cp -v /build/reproducible-path/vg-1.59.0+ds/bin/vg-* /build/reproducible-path/vg-1.59.0+ds/debian/help/ '/build/reproducible-path/vg-1.59.0+ds/bin/vg-avx' -> '/build/reproducible-path/vg-1.59.0+ds/debian/help/vg-avx' '/build/reproducible-path/vg-1.59.0+ds/bin/vg-avx2' -> '/build/reproducible-path/vg-1.59.0+ds/debian/help/vg-avx2' '/build/reproducible-path/vg-1.59.0+ds/bin/vg-plain' -> '/build/reproducible-path/vg-1.59.0+ds/debian/help/vg-plain' '/build/reproducible-path/vg-1.59.0+ds/bin/vg-sse3' -> '/build/reproducible-path/vg-1.59.0+ds/debian/help/vg-sse3' '/build/reproducible-path/vg-1.59.0+ds/bin/vg-sse4.1' -> '/build/reproducible-path/vg-1.59.0+ds/debian/help/vg-sse4.1' '/build/reproducible-path/vg-1.59.0+ds/bin/vg-ssse3' -> '/build/reproducible-path/vg-1.59.0+ds/debian/help/vg-ssse3' export PATH="$PATH:/build/reproducible-path/vg-1.59.0+ds/debian/help" \ ; for SIMD in avx2 avx sse4.1 ssse3 sse3 \ ; do export BIN=/build/reproducible-path/vg-1.59.0+ds/debian/help/vg-${SIMD} \ ; echo "Testing ${BIN}" \ && cp -v "${BIN}" "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg" \ && . /build/reproducible-path/vg-1.59.0+ds/source_me.sh \ && ( cd /build/reproducible-path/vg-1.59.0+ds/test && prove -v t/ ) \ ; if [ $? != 0 ] \ && (lscpu | grep -v ${SIMD}) \ ; then exit 255 \ ; fi \ ; done Testing /build/reproducible-path/vg-1.59.0+ds/debian/help/vg-avx2 '/build/reproducible-path/vg-1.59.0+ds/debian/help/vg-avx2' -> '/build/reproducible-path/vg-1.59.0+ds/debian/help/vg' index file /tmp/vg-KIisg5/vg-zUcrka.fai not found, generating... index file /tmp/vg-KIisg5/vg-ic41h7.fai not found, generating... index file /tmp/vg-KIisg5/vg-gnIBPd.fai not found, generating... index file /tmp/vg-KIisg5/vg-tEGA1U.fai not found, generating... warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;CIPOS=0,3;CIEND=-3,0 GT ! index file /tmp/vg-KIisg5/vg-iAbLwN.fai not found, generating... index file /tmp/vg-KIisg5/vg-t94QNv.fai not found, generating... index file /tmp/vg-KIisg5/vg-J1uKQ2.fai not found, generating... index file /tmp/vg-KIisg5/vg-A16SLv.fai not found, generating... index file /tmp/vg-KIisg5/vg-4edqAi.fai not found, generating... index file /tmp/vg-KIisg5/vg-9wJwx3.fai not found, generating... index file /tmp/vg-KIisg5/vg-B8tGnA.fai not found, generating... index file /tmp/vg-KIisg5/vg-XfpseM.fai not found, generating... index file /tmp/vg-KIisg5/vg-cnFDbp.fai not found, generating... index file /tmp/vg-KIisg5/vg-dKFZi0.fai not found, generating... Warning: deletion END and SVLEN do not agree [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;SVLEN=-19;CIPOS=0,3;CIEND=-3,0;SPAN=19 GT END: 29 SVLEN: -19 warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;SVLEN=-19;CIPOS=0,3;CIEND=-3,0;SPAN=19 GT index file /tmp/vg-KIisg5/vg-2juJJE.fai not found, generating... Warning: deletion END and SVLEN do not agree [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;SVLEN=-19;CIPOS=0,3;CIEND=-3,0;SPAN=19 GT END: 29 SVLEN: -19 warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;SVLEN=-19;CIPOS=0,3;CIEND=-3,0;SPAN=19 GT index file /tmp/vg-KIisg5/vg-oI02Of.fai not found, generating... index file /tmp/vg-KIisg5/vg-d44ywN.fai not found, generating... index file /tmp/vg-KIisg5/vg-IvNRes.fai not found, generating... index file /tmp/vg-KIisg5/vg-ApgW4Q.fai not found, generating... index file /tmp/vg-KIisg5/vg-HeS1yX.fai not found, generating... index file /tmp/vg-KIisg5/vg-4wCKwu.fai not found, generating... index file /tmp/vg-KIisg5/vg-QV4G1Y.fai not found, generating... index file /tmp/vg-KIisg5/vg-zsw1pW.fai not found, generating... index file /tmp/vg-KIisg5/vg-aj4xfB.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;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=18;CIPOS=0,3;SPAN=4 GT END: 18 POS: 9 warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=18;CIPOS=0,3;SPAN=4 GT index file /tmp/vg-KIisg5/vg-p5wpc2.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;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=18;CIPOS=0,3;SPAN=4 GT END: 18 POS: 9 warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=18;CIPOS=0,3;SPAN=4 GT index file /tmp/vg-KIisg5/vg-Z3ZSw9.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;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=13;CIPOS=0,3;SPAN=4 GT END: 13 POS: 9 Warning: VCF writer incorrecty produced END = POS + SVLEN for an insertion. Fixing END to POS. index file /tmp/vg-KIisg5/vg-l3Qqmo.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;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=13;CIPOS=0,3;SPAN=4 GT END: 13 POS: 9 Warning: VCF writer incorrecty produced END = POS + SVLEN for an insertion. Fixing END to POS. index file /tmp/vg-KIisg5/vg-W6UOQz.fai not found, generating... index file /tmp/vg-KIisg5/vg-7ZqOHN.fai not found, generating... index file /tmp/vg-KIisg5/vg-wUHsKm.fai not found, generating... index file /tmp/vg-KIisg5/vg-U2aHcD.fai not found, generating... warning:[vg::Constructor] Lowercase characters found in x; coercing to uppercase. index file /tmp/vg-KIisg5/vg-rupNfA.fai not found, generating... warning:[vg::Constructor] Lowercase characters found in x; coercing to uppercase. index file /tmp/vg-KIisg5/vg-tWiHrs.fai not found, generating... index file /tmp/vg-KIisg5/vg-x5rwwP.fai not found, generating... index file /tmp/vg-KIisg5/vg-GlcFup.fai not found, generating... index file /tmp/vg-KIisg5/vg-ixQ3GM.fai not found, generating... 2 0 3 0 iterated on 4 0 iterated on 5 0 iterated on 7 0 iterated on 8 0 iterated on 7 1 Warning: Cactus does not currently support finding snarls in a single-node connected component warning:[GFAParser] Skipping GFA P line: GFA format error: On pass 2: On line 2: Duplicate path x exists in graph Testing libvgio... warning: distance index uses oversized snarls, which may make mapping slow try increasing --snarl-limit when building the distance index warning: distance index uses oversized snarls, which may make mapping slow try increasing --snarl-limit when building the distance index warning: distance index uses oversized snarls, which may make mapping slow try increasing --snarl-limit when building the distance index warning: distance index uses oversized snarls, which may make mapping slow try increasing --snarl-limit when building the distance index 12 11 WARNING: Excluded 2 transcripts with overlapping exons or incorrect exon order. WARNING: Excluded 2 transcripts with overlapping exons or incorrect exon order. WARNING: Excluded 1 transcripts with exon overlapping a haplotype break. t/00_unittest.t ....... 1..1 =============================================================================== All tests passed (8336883 assertions in 617 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 variants like: z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;END=1017354;NS=2504;SVLEN=-3562;SVTYPE=DEL;DP=15541;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0 ! warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AN=5008;CS=ALU_umary;MEINFO=AluUndef,2,281,+;NS=2504;SVLEN=279;SVTYPE=ALU;TSD=null;DP=18053;EAS_AF=0;AMR_AF=0.0043;AFR_AF=0.0303;EUR_AF=0;SAS_AF=0 ! warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 490168 DUP_gs_CNV_20_1490168_1549769 G 100 PASS AC=1;AF=0.000199681;AN=5008;CS=DUP_gs;END=1549769;NS=2504;SVTYPE=DUP;DP=21874;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0.001 ! Warning: deletion END and SVLEN do not agree [canonicalize] z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;END=1017354;NS=2504;SVLEN=-3562;SVTYPE=DEL;DP=15541;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0;SPAN=3562 END: 1017354 SVLEN: -3562 warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;END=1017354;NS=2504;SVLEN=-3562;SVTYPE=DEL;DP=15541;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0;SPAN=3562 Warning: deletion END and SVLEN do not agree [canonicalize] z 43039 UW_VH_8960 T 100 PASS AC=2;AF=0.000399361;AN=5008;CIEND=0,208;CIPOS=-245,0;CS=DEL_union;END=1044489;NS=2504;SVLEN=-1677;SVTYPE=DEL;DP=18239;EAS_AF=0;AMR_AF=0.0029;AFR_AF=0;EUR_AF=0;SAS_AF=0;SPAN=1677 END: 1044489 SVLEN: -1677 Warning: deletion END and SVLEN do not agree [canonicalize] z 73265 UW_VH_16869 G 100 PASS AC=3;AF=0.000599042;AN=5008;CIEND=0,102;CIPOS=-125,0;CS=DEL_union;END=1077324;NS=2504;SVLEN=-4157;SVTYPE=DEL;DP=19418;EAS_AF=0;AMR_AF=0;AFR_AF=0.0023;EUR_AF=0;SAS_AF=0;SPAN=4157 END: 1077324 SVLEN: -4157 Warning: deletion END and SVLEN do not agree [canonicalize] z 129960 BI_GS_DEL1_B3_P2734_8 A 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-16,16;CIPOS=-16,16;CS=DEL_union;END=1131366;NS=2504;SVLEN=-1405;SVTYPE=DEL;DP=18804;EAS_AF=0;AMR_AF=0;AFR_AF=0.0008;EUR_AF=0;SAS_AF=0;SPAN=1405 END: 1131366 SVLEN: -1405 Warning: deletion END and SVLEN do not agree [canonicalize] z 307697 UW_VH_6096 A 100 PASS AC=2;AF=0.000399361;AN=5008;CIEND=0,82;CIPOS=-77,0;CS=DEL_union;END=1318064;NS=2504;SVLEN=-10447;SVTYPE=DEL;DP=20245;EAS_AF=0.002;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0;SPAN=10447 END: 1318064 SVLEN: -10447 Warning: deletion END and SVLEN do not agree [canonicalize] z 389096 UW_VH_3735 G 100 PASS AC=2647;AF=0.528554;AN=5008;CIEND=0,478;CIPOS=-443,0;CS=DEL_union;END=1390815;NS=2504;SVLEN=-2051;SVTYPE=DEL;DP=18400;EAS_AF=0.7996;AMR_AF=0.5922;AFR_AF=0.2685;EUR_AF=0.5;SAS_AF=0.5849;SPAN=2051 END: 1390815 SVLEN: -2051 Warning: deletion END and SVLEN do not agree [canonicalize] z 405367 BI_GS_DEL1_B3_P2734_19 G 100 PASS AC=2;AF=0.000399361;AN=5008;CIEND=-9,9;CIPOS=-9,9;CS=DEL_union;END=1406601;NS=2504;SVLEN=-1232;SVTYPE=DEL;DP=21506;EAS_AF=0;AMR_AF=0;AFR_AF=0.0015;EUR_AF=0;SAS_AF=0;SPAN=1232 END: 1406601 SVLEN: -1232 Warning: deletion END and SVLEN do not agree [canonicalize] z 557325 UW_VH_21401 G 100 PASS AC=314;AF=0.0626997;AN=5008;CIEND=0,245;CIPOS=-268,0;CS=DEL_union;END=1559946;NS=2504;SVLEN=-2877;SVTYPE=DEL;DP=17241;EAS_AF=0.004;AMR_AF=0.0648;AFR_AF=0.0552;EUR_AF=0.1412;SAS_AF=0.0511;SPAN=2877 END: 1559946 SVLEN: -2877 Warning: deletion END and SVLEN do not agree [canonicalize] z 560739 YL_CN_CHB_4219 T 100 PASS AC=4099;AF=0.81849;AN=5008;CIEND=-500,1000;CIPOS=-1000,500;CS=DEL_union;END=1593685;NS=2504;SVLEN=-32947;SVTYPE=DEL;DP=20713;EAS_AF=0.7867;AMR_AF=0.6527;AFR_AF=0.9213;EUR_AF=0.7903;SAS_AF=0.8589;SPAN=32947 END: 1593685 SVLEN: -32947 Warning: deletion END and SVLEN do not agree [canonicalize] z 596789 BI_GS_DEL1_B1_P2734_566 C 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-11,11;CIPOS=-11,11;CS=DEL_union;END=1600144;NS=2504;SVLEN=-3354;SVTYPE=DEL;DP=16771;EAS_AF=0.001;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0;SPAN=3354 END: 1600144 SVLEN: -3354 Warning: deletion END and SVLEN do not agree [canonicalize] z 599361 BI_GS_DEL1_B2_P2734_449 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-20,20;CIPOS=-20,20;CS=DEL_union;END=1605179;NS=2504;SVLEN=-5817;SVTYPE=DEL;DP=17612;EAS_AF=0;AMR_AF=0;AFR_AF=0.0008;EUR_AF=0;SAS_AF=0;SPAN=5817 END: 1605179 SVLEN: -5817 Warning: deletion END and SVLEN do not agree [canonicalize] z 602412 BI_GS_DEL1_B4_P2734_149 C 100 PASS AC=4;AF=0.000798722;AN=5008;CIEND=-15,15;CIPOS=-15,15;CS=DEL_union;END=1603204;NS=2504;SVLEN=-791;SVTYPE=DEL;DP=21930;EAS_AF=0.002;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0.002;SPAN=791 END: 1603204 SVLEN: -791 Warning: deletion END and SVLEN do not agree [canonicalize] z 670381 UW_VH_15556 T 100 PASS AC=14;AF=0.00279553;AN=5008;CIEND=0,256;CIPOS=-240,0;CS=DEL_union;END=1674237;NS=2504;SVLEN=-4037;SVTYPE=DEL;DP=18965;EAS_AF=0;AMR_AF=0;AFR_AF=0.0106;EUR_AF=0;SAS_AF=0;SPAN=4037 END: 1674237 SVLEN: -4037 Warning: deletion END and SVLEN do not agree [canonicalize] z 995483 UW_VH_2849 T 100 PASS AC=193;AF=0.0385383;AN=5008;CIEND=0,386;CIPOS=-423,0;CS=DEL_union;END=1997552;NS=2504;SVLEN=-2301;SVTYPE=DEL;DP=16520;EAS_AF=0;AMR_AF=0.0461;AFR_AF=0.0454;EUR_AF=0.0547;SAS_AF=0.047;SPAN=2301 END: 1997552 SVLEN: -2301 error:[vg::Constructor] On z, adding reference to last edit end, next end is at 1053404 but reference is only 459552 long warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;END=1017354;NS=2504;SVLEN=-3562;SVTYPE=DEL;DP=15541;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0 ! warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AN=5008;CS=ALU_umary;MEINFO=AluUndef,2,281,+;NS=2504;SVLEN=279;SVTYPE=ALU;TSD=null;DP=18053;EAS_AF=0;AMR_AF=0.0043;AFR_AF=0.0303;EUR_AF=0;SAS_AF=0 ! Restricting to gi|568815592:29791752-29792749 from 1 to end index file sv/x.fa.fai not found, generating... 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..30 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 not ok 7 - vg construct can skip self-inconsistent structural variants # got: '1' # expected: '0' ok 8 - node size is manageable by default ok 9 - construction of a very complex region succeeds ok 10 - the complex graph has the expected number of nodes ok 11 - the complex graph has the expected number of edges ok 12 - the ordering of variants at the same position has no effect on the resulting graph ok 13 - construction does not fail when the first position in the VCF is repeated and has an indel ok 14 - the size of the regions used in construction has no effect on the graph ok 15 - the number of threads used in construction has no effect on the graph ok 16 - the number of threads and regions used in construction has no effect on the graph ok 17 - construction of a graph with two head nodes succeeds ok 18 - the graph contains all the sequence in the reference and VCF ok 19 - varying the max node size does not affect graph length ok 20 - nodes are correctly capped in size ok 21 - -R --region flag is respected ok 22 - vg construct does not require a vcf ok 23 - vg construct respects node size limit ok 24 - --region can be interpreted to be a reference sequence (and not parsed as a region spec) ok 25 - vg constructs the correct graph for inversions ok 26 - vg construct skips variants with . ALTs ok 27 - VCF with * alleles is accepted ok 28 - VCF record with * allele is rejected ok 29 - Reference with ambiguity codes has them coerced to Ns ok 30 - Expected number of Ns are created Failed 1/30 subtests [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. error[VPKG::load_one]: Could not open test/graphs/rgfa_with_reference.rgfa while loading handlegraph::PathHandleGraph error:[get_input_file_name] unable to open input file: test/graphs/rgfa_with_reference.rgfa error[VPKG::load_one]: Could not open test/graphs/rgfa_with_reference.rgfa while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Could not open test/graphs/gfa_with_reference.gfa while loading handlegraph::PathHandleGraph error:[get_input_file_name] unable to open input file: test/graphs/gfa_with_reference.gfa error[VPKG::load_one]: Could not open test/graphs/gfa_with_reference.gfa while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph t/03_vg_view.t ........ 1..23 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 ok 5 - view can round-trip JSON and GAM ok 6 - view can round-trip qualities and encodes tham as PHRED+0 base-64-encoded strings in JSON ok 7 - view can reconstruct a VG graph from JSON ok 8 - view can pass through VG when loading as vg::VG ok 9 - view can pass through semantically identical VG normally ok 10 - view parses sample names ok 11 - view can handle fastq input ok 12 - view can translate graphs with 2-node cycles ok 13 - view outputs properly oriented GFA ok 14 - view produces the expected number of lines of dot output from a cyclic graph ok 15 - streaming JSON output produces the expected number of chunks ok 16 - duplicate warnings can be suppressed when loading as vg::VG ok 17 - gfa graphs with overlaps are rejected ok 18 - GFA import produces a concise error message when overlaps are present ok 19 - GFA import rejects a GFA file with an overlap that goes beyond its sequences ok 20 - GFA import produces a concise error message in that case ok 21 - vg view preserves path metadata of rGFA file ok 22 - vg view preserves path metadata of GFA file ok 23 - vg view can emit a GFA file with subranges on a haplotype without explicit phase blocks ok [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 [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. t/05_vg_find.t ........ 1..29 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 ok 21 - extracting by path adds no extra edges ok 22 - pattern based path extraction works 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 ok 28 - GFA i/o for find -n consistent with converting both ways ok 29 - find nodes that map to the provided node ids ok WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. warning: -i option is deprecated WARNING:[vg] Subcommand 'concat' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. t/06_vg_index.t ....... 1..54 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 piped vg graph ok 52 - building a distance index of a piped PackedGraph ok 53 - distance index construction from GBZ ok 54 - distance index construction from piped GBZ ok warning: Thread 0 encountered sequence of length 100, which is longer than the non-chunked limit of 30. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [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 warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. index file t.fa.fai not found, generating... [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. t/07_vg_map.t ......... 1..55 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 - vg can map multi-line FASTA sequences ok 21 - mapping of BAM file produces expected number of alignments ok 22 - mapping from a fastq produces the expected number of alignments ok 23 - allowing secondary alignments with MEM mapping does not change number of primary alignments ok 24 - vg connects paired-end reads in gam output ok 25 - mapping to graphs that can't be oriented without swapping edges works correctly ok 26 - reads multi-map to multiple possible locations ok 27 - vg map works based on gcsa and xg indexes ok 28 - the mapping quality may be capped ok 29 - paired read alignments forced to be consistent have lower score than unrestricted alignments ok 30 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments ok 31 - only primary alignments have mapping quality scores ok 32 - unpaired reads produce mapping quality scores ok 33 - map returns same output on xg and vg (single threaded) ok 34 - base quality adjusted alignment produces higher scores if mismatches have low quality ok 35 - error on vg map -f (unpaired) ok 36 - error on vg map -f (interleaved) ok 37 - error on vg map -f (paired, LHS) ok 38 - error on vg map -f (paired, RHS) ok 39 - mapping a read that touches unused nodes gets the base score ok 40 - mapping a read that matches a haplotype gets a small penalty ok 41 - mapping a read that matches a haplotype with exponent 0 gets the base score ok 42 - mapping a read that matches no haplotypes gets a larger penalty ok 43 - surjection of paired reads to SAM yields correct positions ok 44 - surjection of paired reads to SAM yields correct pair partner positions ok 45 - surjection of paired reads to SAM yields properly matched QNAMEs ok 46 - surjection of paired reads to SAM produces correct pair partner contigs ok 47 - surjection of paired reads to SAM produces correct flags ok 48 - surjection of unpaired reads to SAM yields correct positions ok 49 - surjection of unpaired reads to SAM yields correct pair partner positions ok 50 - surjection of unpaired reads to SAM yields distinct QNAMEs ok 51 - surjection of unpaired reads to SAM produces absent partner contigs ok 52 - surjection of unpaired reads to SAM produces correct flags ok 53 - mapper can read FASTA input ok 54 - mapper can read multiline FASTA input ok 55 - xdrop works on a reversed read ok [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. 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 WARNING:[vg] Subcommand 'concat' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'concat' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. WARNING:[vg] Subcommand 'concat' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'concat' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. 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 ok 4 - concat -p doubles the number of edges + 1 on reversing graph ok t/100_code_quality.t .. 1..1 ok 1 - code quality is acceptable ok warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;END=1017354;NS=2504;SVLEN=-3562;SVTYPE=DEL;DP=15541;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0 ! warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AN=5008;CS=ALU_umary;MEINFO=AluUndef,2,281,+;NS=2504;SVLEN=279;SVTYPE=ALU;TSD=null;DP=18053;EAS_AF=0;AMR_AF=0.0043;AFR_AF=0.0303;EUR_AF=0;SAS_AF=0 ! warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 490168 DUP_gs_CNV_20_1490168_1549769 G 100 PASS AC=1;AF=0.000199681;AN=5008;CS=DUP_gs;END=1549769;NS=2504;SVTYPE=DUP;DP=21874;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0.001 ! [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg autoindex] Executing command: vg autoindex -v tiny/tiny.vcf.gz -r tiny/tiny.fa -w giraffe -p tiny [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Downsampling full GBWT. [IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. [IndexRegistry]: Constructing GBZ. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. warning:[GFAParser] Ignoring unrecognized # line type t/10_vg_stats.t ....... 1..21 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 xg graph ok 17 - vg stats -F detects format of GFA graph ok 18 - vg stats -F detects format of GBZ graph ok 19 - vg stats -D found correct degree distribution of tiny graph ok 20 - vg stats -L counts self-loops correctly ok 21 - vg stats -e finds the right nondeterministic edge sets 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: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. 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: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. 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: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. 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: Thread 0 encountered sequence of length 68, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 54, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. t/11_vg_paths.t ....... 1..20 ok 1 - path listing works from vg ok 2 - path listing works from XG ok 3 - generic path listing works from XG ok 4 - thread listing works from GBWT ok 5 - haplotype thread listing works from GBWT ok 6 - thread selection by name prefix works correctly ok 7 - thread selection by sample name works correctly ok 8 - no threads are reported for invalid samples ok 9 - vg paths may be used to extract threads ok 10 - vg paths may be used to extract threads as GAF ok 11 - Fasta extracted from xg is the same as the input fasta ok 12 - Fasta extracted from vg is the same as the input fasta ok 13 - Fasta extracted from threads has correct number of lines ok 14 - a single path may be retained ok 15 - path filtering does not modify the graph ok 16 - alt allele paths can be dropped ok 17 - vg path coverage has correct number of columns ok 18 - vg path coverage has correct number of rows ok 19 - vg paths found correct number of lengths ok 20 - vg path coverage reports correct lengths in first column 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 mod]: -o is deprecated. Dangling edges are now automatically removed.[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. 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 [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. t/13_vg_sim.t ......... 1..36 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 - All reads are annotated with single reference positions by default ok 34 - All reads can be annotated with multiple reference positions when requested ok 35 - ngs trained simulator works ok 36 - 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 [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. graph: valid [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 graph: valid graph: valid [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 [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [algorithms::normalize] iteration 1 current length 95 [algorithms::normalize] iteration 2 current length 95 [algorithms::normalize] normalized in 1 steps [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. graph: valid 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: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid 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: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. graph: valid [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [algorithms::normalize] iteration 1 current length 100 [algorithms::normalize] iteration 2 current length 100 [algorithms::normalize] normalized in 1 steps graph: valid [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [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. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. 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: Thread 0 encountered sequence of length 100, which is longer than the non-chunked limit of 16. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. 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: Thread 0 encountered sequence of length 70, which is longer than the non-chunked limit of 16. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid [algorithms::normalize] iteration 1 current length 5 [algorithms::normalize] normalized in 0 steps graph: valid [algorithms::normalize] iteration 1 current length 5 [algorithms::normalize] normalized in 0 steps graph: valid 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 'WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely.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. graph: valid WARNING:[vg] Subcommand 'kmersWARNING:[vg] Subcommand '' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely.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. graph: valid graph: valid 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: Thread 0 encountered sequence of length 200, which is longer than the non-chunked limit of 19. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 19. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [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 warning: Thread 0 encountered sequence of length 200, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [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 ok 13 - chopping a graph works correctly with reverse mappings ok 14 - unchop correctly handles paths ok 15 - unchop correctly handles a graph with an inversion ok 16 - unchop handles doubly-reversing edges 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 ok warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg mpmap] It is HIGHLY recommended to use a distance index (-d) for clustering on splice graphs. Both accuracy and speed will suffer without one. warning:[vg mpmap] It is HIGHLY recommended to use a distance index (-d) for clustering on splice graphs. Both accuracy and speed will suffer without one. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. index file x.sub.fa.fai not found, generating... warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x x.xg -g x.gcsa -n dna --suppress-mismapping -B -G x.gam -i -F GAM -I 60 -D 10 [vg mpmap] elapsed time 0 s: Loading graph from x.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Loading GCSA2 from x.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from x.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from x.gam using 42 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x x.xg -g x.gcsa -n dna --suppress-mismapping -B -G x.gam -i -F GAMP -I 60 -D 10 [vg mpmap] elapsed time 0 s: Loading graph from x.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Loading GCSA2 from x.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from x.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from x.gam using 42 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 read pairs. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. t/15_vg_surject.t ..... 1..47 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 reports alignment scores ok 7 - vg surject picks a reference-sense path if it is present ok 8 - vg surject works for every read simulated from a dense graph ok 9 - vg surject spliced algorithm works for every read simulated from a dense graph ok 10 - vg surject produces valid SAM output ok 11 - vg map may surject reads to produce valid SAM output ok 12 - vg map may surject reads to produce valid BAM output ok 13 - vg surject retains read names ok 14 - vg surject can set sample and read group ok 15 - we respect the original mapping's softclips ok 16 - quality strings we will use for testing are oriented correctly ok 17 - forward and reverse orientations of a read produce the same surjected SAM, ignoring flags ok 18 - vg surject produces valid BAM output ok 19 - mapping quality is preserved through surjection ok 20 - read pairing is preserved through GAM->GAM surjection ok 21 - interleaved surjection produces same SAM when using GAF and GAM inputs ok 22 - surjection of paired reads to SAM yields correct positions ok 23 - surjection of paired reads to SAM yields correct pair partner positions ok 24 - surjection of paired reads to SAM yields properly matched QNAMEs ok 25 - surjection of paired reads to SAM produces correct pair partner contigs ok 26 - surjection of paired reads to SAM produces correct flags ok 27 - surjection of paired reads to SAM tags both reads with a read group ok 28 - surjection of paired reads to SAM creates RG header ok 29 - surjection works for a longer (151bp) read ok 30 - surjection works for another difficult read ok 31 - mapping reproduces qualities from BAM input ok 32 - mapping reproduces qualities from fastq input ok 33 - mapping reproduces qualities from GAF input ok 34 - surject works on GAMP input ok 35 - surject works on paired GAMP input ok 36 - vg surject correctly handles subpath suffix in path name ok 37 - vg surject correctly fetches base path length from input file ok 38 - vg surject does not crash when surjecting a read that grazes the reference with a deletion ok 39 - vg surject leaves a read that grazes the reference with a deletion unmapped ok 40 - vg surject does not crash when surjecting a read that grazes the reference with a deletion and pruning low complexity anchors ok 41 - vg surject leaves a read that grazes the reference with a deletion unmapped when pruning low complexity anchors ok 42 - GAM surject can return only primaries ok 43 - GAM surject can return multimappings ok 44 - GAM surject can return paired multimappings ok 45 - GAMP surject can return only primaries ok 46 - GAMP surject can return multimappings ok 47 - GAMP surject can return multimappings 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: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [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. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [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. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 16. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [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 in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input 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 in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input 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: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [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... warning: Thread 0 encountered sequence of length 100, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [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: Thread 0 encountered sequence of length 49, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid 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: Thread 0 encountered sequence of length 3186, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3186, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3186, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3186, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3184, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3183, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3182, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3181, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid 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: Thread 0 encountered sequence of length 200, which is longer than the non-chunked limit of 64. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid 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... warning: Thread 0 encountered sequence of length 210, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [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: Thread 0 encountered sequence of length 70, which is longer than the non-chunked limit of 16. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid 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: Thread 0 encountered sequence of length 3365, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3364, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3343, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3341, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3341, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3341, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3341, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3340, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid 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: Thread 0 encountered sequence of length 210, which is longer than the non-chunked limit of 16. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid 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": "7", "from_start": true, "to": "8", "to_end": true}, {"from": "1", "to": "8"}, {"from": "1", "to": "7"}], "node": [{"id": "7", "sequence": "GGACTAAGGACAAAGGTGCGGGGAG"}, {"id": "8", "sequence": "AACTACTCCACATCAAAGCTACCCAGGCCATTTTAAGTTTCCTGT"}, {"id": "1", "sequence": "TCAGATTCTCATCCCTCCTCAAGGGCTTCT"}], "path": [{"mapping": [{"edit": [{"from_length": 30, "to_length": 30}], "position": {"node_id": "1"}, "rank": "1"}, {"edit": [{"from_length": 45, "to_length": 45}], "position": {"node_id": "8"}, "rank": "2"}, {"edit": [{"from_length": 25, "to_length": 25}], "position": {"node_id": "7"}, "rank": "3"}], "name": "s1"}, {"mapping": [{"edit": [{"from_length": 30, "to_length": 30}], "position": {"node_id": "1"}, "rank": "1"}, {"edit": [{"from_length": 25, "to_length": 25}], "position": {"node_id": "7"}, "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 [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg augment] warning: -a / --augmentation-mode option is deprecated [vg augment] warning: -a / --augmentation-mode option is deprecated [vg augment] warning: -a / --augmentation-mode option is deprecated [vg augment] warning: -a / --augmentation-mode option is deprecated [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 view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [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 ok 1 - direct augmentation embeds reads fully for well-supported SNPs ok 2 - adding a well-supported SNP by direct augmentation adds 3 more nodes ok 3 - adding a well-supported SNP by direct augmentation adds 3 more nodes with -m 1 ok 4 - direct augmentation embeds with GAF reads fully for well-supported SNPs ok 5 - adding a well-supported SNP by direct augmentation with GAF adds 3 more nodes ok 6 - direct augmentation embeds reads fully for probable errors ok 7 - adding a probable error by direct augmentation adds 3 more nodes 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 ok [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. 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. warning: Thread 0 encountered sequence of length 200, which is longer than the non-chunked limit of 64. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. index file m.fa.fai not found, generating... [vg autoindex] Executing command: vg autoindex -r small/x.fa -v small/x.vcf.gz -w giraffe -p x [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Downsampling full GBWT. [IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. [IndexRegistry]: Constructing GBZ. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. index file x_sub1.fa.fai not found, generating... index file x_sub2.fa.fai not found, generating... t/18_vg_call.t ........ 1..19 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 13 - call produces same output with gbwt and gbz ok 14 - vg call makes currect base path header with subpath input ok 15 - vg call makes only currect base path header with subpath input ok 16 - vg call only reports base paths with subpath input ok 17 - vg call makes currect base path header with subpath input and override ok 18 - vg call makes only currect base path header with subpath input and override ok 19 - overriding contig length does not change calls 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 warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x g.xg -g g.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -I 10 -D 50 -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from g.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Loading GCSA2 from g.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from g.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x g.xg -g g.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -I 10 -D 1 -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from g.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Loading GCSA2 from g.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from g.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. t/21_vg_filter.t ...... 1..13 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 - properly paired read passes proper filter ok 10 - improperly paired read fails proper filter ok 11 - read pairs can be tropped by feature ok 12 - read pairs can be kept if only one read fails ok 13 - unmapped reads can be filtered out ok t/22_ggsv.t ........... skipped: (no reason given) t/23_vectorize.t ...... skipped: (no reason given) [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. 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. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 1014 [algorithms::normalize] normalized in 0 steps Warning [vg deconstruct]: -e is deprecated as it's now on default [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. Warning [vg deconstruct]: -e is deprecated as it's now on default Warning [vg deconstruct]: -e is deprecated as it's now on default [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. Warning [vg deconstruct]: -e is deprecated as it's now on default Warning [vg deconstruct]: -e is deprecated as it's now on default [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. Warning [vg deconstruct]: -e is deprecated as it's now on default [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. Warning [vg deconstruct]: -H is deprecated, and will be ignored Warning [vg deconstruct]: -e is deprecated as it's now on default Warning [vg deconstruct]: -d is deprecated - ploidy now inferred from haplotypes in path names Warning [vg deconstruct]: -H is deprecated, and will be ignored Warning [vg deconstruct]: -e is deprecated as it's now on default Warning [vg deconstruct]: -d is deprecated - ploidy now inferred from haplotypes in path names t/26_deconstruct.t: line 127: bcftools: command not found t/26_deconstruct.t: line 128: bcftools: command not found t/26_deconstruct.t: line 129: bcftools: command not found t/26_deconstruct.t: line 130: bcftools: command not found [vg autoindex] Executing command: vg autoindex -r small/x.fa -v small/x.vcf.gz -w giraffe -p x [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Downsampling full GBWT. [IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. [IndexRegistry]: Constructing GBZ. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. t/26_deconstruct.t .... 1..37 ok 1 - deconstructed hla vcf has correct number of sites ok 2 - deconstructed hla vcf has correct insertion ok 3 - deconstructed hla vcf with other path has correct number of sites ok 4 - deconstructed hla vcf has correct deletion ok 5 - path-based and exhaustive decontruction give equivalent sites when expected ok 6 - path that differs from reference in every alt has correct genotype ok 7 - path that is same as reference in every alt has correct genotype ok 8 - reference contig correctly written ok 9 - deconstruct correctly handles a simple inversion ok 10 - deconstruct correctly handles a simple inversion when the reference contains the reversing edge ok 11 - deconstruct applies translation from gbz with -O 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 -H options return correct number of variants ok 17 - -P -H options use correct reference name ok 18 - -P -H does not find conflict in alt1 in second variant ok 19 - deconstructing vg graph gives same output as xg graph ok 20 - haplotype 1 preserved when deconstructing small test with gbwt ok 21 - haplotype 2 preserved when deconstructing small test with gbwt ok 22 - gbz deconstruction gives same output as gbwt deconstruction ok 23 - cluster-free deconstruction finds all alt alleles ok 24 - clustered deconstruction finds fewer alt alleles ok 25 - clustered deconstruction finds correct allele info ok 26 - nested deconstruction gets correct star-allele for snp inside deletion ok 27 - PA=0 correctly set at both sites of neseted deletion ok 28 - nested deconstruction gets correct allele for snp inside deletion (without -R) ok 29 - nested deconstruction gets correct allele for snp inside insert ok 30 - PA=0 set for base allele of nested insertion ok 31 - PA=1 set for nested allele of nested insertion ok 32 - nested deconstruction gets correct contigs in vcf header for snp inside insert ok 33 - nested deconstruction gets correct star allele for snp ins2.ide ins2.ert ok 34 - INFO tags correct for level-0 site of double-nested SNP ok 35 - INFO tags correct for level-1 site of double-nested SNP ok 36 - INFO tags correct for level-2 site of double-nested SNP ok 37 - nested deconstruction handles cycle 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: 2 1 1 3 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... Warning: realigned read TATGTCTGTAGG doesn't touch either end of its snarl! Warning: realigned read CCCTACAGACAT doesn't touch either end of its snarl! Warning: realigned read GAGCCCTACAGA doesn't touch either end of its snarl! Warning: realigned read CTCATTGTAACG doesn't touch either end of its snarl! Warning: realigned read CTGTAGGGCTCA doesn't touch either end of its snarl! Warning: realigned read GGGCTCATTGTA doesn't touch either end of its snarl! Warning: realigned read AGGGCTCATTGT doesn't touch either end of its snarl! Warning: realigned read CCTACAGACATA 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 TAGGGCTCATTG doesn't touch either end of its snarl! Warning: realigned read GTTACAATGAGC doesn't touch either end of its snarl! Warning: realigned read TACAATGAGCCC doesn't touch either end of its snarl! Warning: realigned read GTCTGTAGGGCT 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 TACAATGAGCCC doesn't touch either end of its snarl! Warning: realigned read ACGTTACAATGA doesn't touch either end of its snarl! Warning: realigned read GCTCATTGTAAC 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 GTAGGGCTCATT 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 WARNING:[vg] Subcommand 'translate' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. [algorithms::normalize] iteration 1 current length 57 [algorithms::normalize] normalized in 0 steps [algorithms::normalize] iteration 1 current length 57 [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. 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 ok 2 - translation overlay works and produces a sane result ok [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. warning[vg chunk]: the vg-protobuf format is DEPRECATED. you probably want to use PackedGraph (pg) instead [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 [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. t/30_vg_chunk.t ....... 1..32 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 can be found from GBZ ok 5 - snarl chunk works on simple example ok 6 - chunk has path going through node 9 ok 7 - -s produces correct number of chunks ok 8 - gam chunker produces correct number of graphs ok 9 - gam chunker produces correct number of gams ok 10 - gam chunker produces bed with correct number of chunks ok 11 - gam chunker emits each matching read at most once ok 12 - chunk contains the expected number of alignments ok 13 - simple gam chunker produces correct number of gams ok 14 - simple chunk contains the expected number of alignments ok 15 - id chunker produces correct chunk size ok 16 - id chunker produces correct single chunk ok 17 - id chunker traces correct chunk size without haplotypes ok 18 - id chunker traces correct chunk size ok 19 - chunker extracts no threads from an empty gPBWT ok 20 - chunker extracts 2 local threads from a gBWT with 2 locally distinct threads in it ok 21 - chunker can extract a partial haplotype from a GBWT ok 22 - chunker can extract a partial haplotype from a GBZ ok 23 - chunker doesn't see haplotypes in the GBZ if asked not to ok 24 - trace consistent on path coordinates ok 25 - n-chunking works and chunks over the full graph ok 26 - path-based components finds subgraphs ok 27 - x gam chunk has correct number of reads ok 28 - y gam chunk has correct number of reads ok 29 - x gam chunk has correct number of reads with -p path ok 30 - y gam chunk has correct number of reads with -p path ok 31 - path-based component contains correct path length ok 32 - components finds subgraphs ok index file add/ref.fa.fai not found, generating... WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. 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 WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. 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 WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. 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 WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. 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... WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. 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... WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. 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 WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. 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 [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead.WARNING:[vg] Subcommand ' add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. 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 [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead.WARNING:[vg] Subcommand ' add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. 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 4: 3 haplotypes at ref3:18: 32 bp vs. 34 bp haplotypes vs. graphs average Variant 5: 3 haplotypes at ref3:21: 32 bp vs. 34 bp haplotypes vs. graphs average Variant 6: 3 haplotypes at ref3:23: 33 bp vs. 34 bp haplotypes vs. graphs average WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. 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 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 ok 10 - graphs with backward nodes can be added to ok 11 - graphs with multiple overlapping paths nodes can be added to ok 12 - graphs with backward and forward nodes can be added to ok [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. Restricting to x from 1 to end Restricting to y from 1 to end [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg autoindex] Executing command: vg autoindex -p index -g graphs/big_snarl_named.gfa -w giraffe [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing VG graph from GFA input. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Constructing a greedy path cover GBWT [IndexRegistry]: Constructing GBZ using NamedNodeBackTranslation. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. t/32_vg_snarls.t ...... 1..19 ok 1 - vg snarls made right number of protobuf Snarls ok 2 - vg snarls made right number of protobuf SnarlTraversals ok 3 - vg snarls made snarls in the right order ok 4 - vg snarls on xg made right number of protobuf Snarls ok 5 - vg snarls on xg made right number of protobuf SnarlTraversals ok 6 - vcf traversals are the same as exhaustive traversals for tiny graph ok 7 - vcf traversals are the same as exhaustive traversals for inversion ok 8 - vcf traversals are the same as exhaustive traversals for ins_and_del graph ok 9 - correct number of snarls when parallelizing on compoents ok 10 - same number of snarls when parallelizing on components ok 11 - GBZ graphs can be used for finding snarls ok 12 - correct number of snarls in the GFA W-line example ok 13 - vg snarls made the right snarls when dealing with nested chains ok 14 - vg snarls made snarls in the right order when dealing with nested chains ok 15 - Correct snarls are found in GFA space ok 16 - In node ID space traversal visits 7 nodes ok 17 - In node ID space traversal visits 4 trivial snarls ok 18 - In segment name space traversal visits 3 segments ok 19 - In segment name space traversal visits 0 trivial snarls ok [vg mpmap] elapsed time 0 s: Executing command: vg mpmap --suppress-mismapping -B -P 1 -n dna -x xy2.xg -g xy2.gcsa -f reads/xy2.match.fq -F GAM [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.match.fq using 42 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap --suppress-mismapping -B -P 1 -n dna -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -f reads/xy2.match.fq -F GAM [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0 s: Completed loading GBWT [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.match.fq using 42 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. warning:[vg mpmap] It is HIGHLY recommended to use a distance index (-d) for clustering on splice graphs. Both accuracy and speed will suffer without one. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap --suppress-mismapping -B -M 2 -n rna -x xy2.xg -g xy2.gcsa -f reads/xy2.match.fq [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.match.fq using 42 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -I 200 -D 200 -x xy2.xg -g xy2.gcsa -f reads/xy2.matchpaired.fq -i -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.matchpaired.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -I 200 -D 200 -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -f reads/xy2.matchpaired.fq -i -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0 s: Completed loading GBWT [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.matchpaired.fq using 1 thread [vg mpmap] elapsed time 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 s: Executing command: vg mpmap -B -P 1 -n dna -x xy2.xg -g xy2.gcsa -s xy2.snarls -f reads/xy2.discordant.fq -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.discordant.fq using 1 thread [vg mpmap] elapsed time 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 s: Executing command: vg mpmap -B -P 1 -n dna -x xy2.xg -g xy2.gcsa -s xy2.snarls -f reads/xy2.discordant.fq -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.discordant.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -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 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Loading snarls from xy2.snarls [vg mpmap] elapsed time 0 s: Completed loading snarls [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0 s: Completed loading GBWT [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.discordant.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -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 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Loading snarls from xy2.snarls [vg mpmap] elapsed time 0 s: Completed loading snarls [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0 s: Completed loading GBWT [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.discordant.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 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 -n dna -B -i -I 10 -D 50 -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 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 -n dna -B -i -I 100000 -D 5 -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 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 -n dna -B -i -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread 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 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 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 -n dna -i -F GAM --no-qual-adjust [vg mpmap] elapsed time 0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from input.gam using 42 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1000 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -n dna -x t.xg -g t.gcsa -f t.fq [vg mpmap] elapsed time 0 s: Loading graph from t.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Loading GCSA2 from t.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from t.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1 s: Mapping reads from t.fq using 42 threads [vg mpmap] elapsed time 1 s: Mapping finished. Mapped 3 reads. [vg mpmap] elapsed time 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 s: Loading graph from s.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0 s: Loading distance index from s.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Mapping reads from s.fq using 42 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 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 s: Loading graph from s.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0 s: Loading distance index from s.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 1 s: Mapping reads from s.fq using 42 threads [vg mpmap] elapsed time 1 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 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 s: Loading graph from s.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0 s: Loading distance index from s.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Mapping reads from s.fq using 42 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 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 -F SAM --report-group-mapq [vg mpmap] elapsed time 0 s: Loading graph from s.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0 s: Loading distance index from s.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: No reference path file given. Interpreting all non-alt-allele paths in graph as reference sequences. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg mpmap] elapsed time 0 s: Mapping reads from s.fq using 42 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x xy.xg -d xy.dist -g xy.gcsa -G x.gam -F SAM -i --frag-mean 50 --frag-stddev 10 -M 1 [vg mpmap] elapsed time 0 s: Loading graph from xy.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy.gcsa [vg mpmap] elapsed time 0 s: Loading distance index from xy.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading LCP from xy.gcsa.lcp [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: No reference path file given. Interpreting all non-alt-allele paths in graph as reference sequences. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg mpmap] elapsed time 0 s: Building null model to calibrate mismapping detection [vg mpmap] elapsed time 8 s: Mapping reads from x.gam using 42 threads [vg mpmap] elapsed time 8 s: Mapping finished. Mapped 1000 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x xy.xg -d xy.dist -g xy.gcsa -G x.gam -F SAM -M 1 [vg mpmap] elapsed time 0 s: Loading graph from xy.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy.gcsa [vg mpmap] elapsed time 0 s: Loading distance index from xy.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading LCP from xy.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: No reference path file given. Interpreting all non-alt-allele paths in graph as reference sequences. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg mpmap] elapsed time 0 s: Building null model to calibrate mismapping detection [vg mpmap] elapsed time 10 s: Mapping reads from x.gam using 42 threads [vg mpmap] elapsed time 10 s: Mapping finished. Mapped 2000 reads. t/33_vg_mpmap.t ....... 1..21 ok 1 - MAPQ is 50% without haplotype info ok 2 - haplotype match can disambiguate ok 3 - MAPQs are computed for all multimappings ok 4 - MAPQ is 50% when paired without haplotype info ok 5 - haplotype match can disambiguate paired ok 6 - use of haplotype-aware mapping is recorded ok 7 - Haplotype-oblivious mapping places read on the wrong contig ok 8 - Haplotype-oblivious mapping places read with MAPQ of 50% ok 9 - Haplotype-aware mapping places read on the right contig ok 10 - Haplotype-aware mapping places read with MAPQ > 50% ok 11 - paired read alignments forced to be consistent have lower score than unrestricted alignments ok 12 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments ok 13 - paired read alignments forced to be near each other are closer together in node id space than those forced to be far apart ok 14 - small batches are still all paired in the output ok 15 - multipath mapping works in scenarios that trigger branch point trimming ok 16 - spliced alignments can be found when aligning RNA ok 17 - paired mapping can identify a splice junction on read 1 ok 18 - paired mapping can identify a splice junction on read 2 ok 19 - HTS output contains group mapq annotation ok 20 - paired reads are evenly split between equivalent mappings ok 21 - unpaired reads are evenly split between equivalent mappings ok [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. t/34_vg_pack.t ........ 1..20 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 ok 18 - average node qualities are correct ok 19 - pack -s 10 sets fist and last 10bp of coverage to 0 like expected ok 20 - pack -s 9 sets fist and last 9bp of coverage to 0 like expected ok [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. 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 ok 9 - annotations derived from BED can span the end/start joins of circular paths ok t/37_vg_gbwt.t ........ 1..159 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 - r-index construction ok 49 - normal merging: non-empty + empty ok 50 - the index remains unchanged ok 51 - normal merging: empty + non-empty ok 52 - the index remains unchanged ok 53 - fast merging: non-empty + empty ok 54 - the index remains unchanged ok 55 - fast merging: empty + non-empty ok 56 - the index remains unchanged ok 57 - parallel merging: non-empty + empty ok 58 - the index remains unchanged ok 59 - parallel merging: empty + non-empty ok 60 - the index remains unchanged ok 61 - haplotypes and paths: 6 threads ok 62 - samples can be removed from a GBWT index ok 63 - haplotypes only: 4 threads ok 64 - all samples: 12 threads ok 65 - all samples: 6 haplotypes ok 66 - multiple samples can be removed from a GBWT index ok 67 - sample 2: 4 threads ok 68 - sample 2: 2 haplotypes ok 69 - threads can be extracted from GBWT ok 70 - correct size for the thread file ok 71 - GBWTGraph construction ok 72 - GBWTGraph was serialized correctly ok 73 - GBZ construction from GBWT ok 74 - GBZ was serialized correctly ok 75 - GBZ construction from VCF ok 76 - Identical construction results from GBWT and VCF ok 77 - GBZ construction from GBWTGraph ok 78 - Identical construction results from XG and GBWTGraph ok 79 - GBWT extraction from GBZ ok 80 - Identical GBWT indexes ok 81 - GBWT + GBWTGraph extraction from GBZ ok 82 - Identical GBWT indexes ok 83 - Identical GBWTGraphs ok 84 - Path cover GBWTGraph construction ok 85 - GBWTGraph was serialized correctly ok 86 - path cover: 32 threads ok 87 - path cover: 2 contigs ok 88 - path cover: 16 haplotypes ok 89 - path cover: 16 samples ok 90 - Path cover GBWTGraph construction ok 91 - GBWTGraph was serialized correctly ok 92 - path cover w/ paths: 34 threads ok 93 - path cover w/ paths: 2 contigs ok 94 - path cover w/ paths: 17 haplotypes ok 95 - path cover w/ paths: 17 samples ok 96 - Local haplotypes GBWTGraph construction ok 97 - GBWTGraph was serialized correctly ok 98 - local haplotypes: 32 threads ok 99 - local haplotypes: 2 contigs ok 100 - local haplotypes: 16 haplotypes ok 101 - local haplotypes: 16 samples ok 102 - Local haplotypes GBZ construction (single job) ok 103 - GBZ was serialized correctly ok 104 - Local haplotypes GBZ construction (two jobs) ok 105 - GBZ was serialized correctly ok 106 - Local haplotypes GBWTGraph construction ok 107 - GBWTGraph was serialized correctly ok 108 - local haplotypes w/ paths: 34 threads ok 109 - local haplotypes w/ paths: 2 contigs ok 110 - local haplotypes w/ paths: 17 haplotypes ok 111 - local haplotypes w/ paths: 17 samples ok 112 - Local haplotypes with reference paths from a larger GBZ ok 113 - local haplotypes w/ paths: 36 threads ok 114 - local haplotypes w/ paths: 2 contigs ok 115 - local haplotypes w/ paths: 18 haplotypes ok 116 - local haplotypes w/ paths: 18 samples ok 117 - local haplotypes w/ paths: reference_samples set ok 118 - Augmented GBWTGraph construction ok 119 - GBWTGraph was serialized correctly ok 120 - augmented: 18 threads ok 121 - augmented: 2 contigs ok 122 - augmented: 18 haplotypes ok 123 - augmented: 17 samples ok 124 - GBWT construction from GFA ok 125 - GBWT was serialized correctly ok 126 - gfa: 4 threads ok 127 - gfa: 2 contigs ok 128 - gfa: 2 haplotypes ok 129 - gfa: 1 sample ok 130 - GBWT+GBWTGraph construction from GFA ok 131 - Identical construction results with and without GBWTGraph ok 132 - GBWTGraph was serialized correctly ok 133 - no chopping: 0 translations ok 134 - GBZ construction from GFA ok 135 - GBZ was serialized correctly ok 136 - GBWT+GBWTGraph construction from GFA with chopping ok 137 - chopping: 3 threads ok 138 - chopping: 1 contig ok 139 - chopping: 3 haplotypes ok 140 - chopping: 2 samples ok 141 - chopping: 9 translations ok 142 - Translation can be extracted from GBZ ok 143 - from GBZ: 8 translations ok 144 - GBWT+GBWTGraph construction from GFA with reference paths ok 145 - ref paths: 6 threads ok 146 - ref paths: 2 contigs ok 147 - ref paths: 3 haplotypes ok 148 - ref paths: 2 samples ok 149 - ref paths: 0 translations ok 150 - GBZ construction from GFA with reference ok 151 - GBZ GBWT tag extraction works ok 152 - GBWT tags contain the correct reference samples ok 153 - GBZ GBWT tag modification works ok 154 - Changing reference_samples tag can make a reference a haplotype ok 155 - Changing reference_samples tag can make a haplotype a reference ok 156 - GBZ GBWT tag modification validation works ok 157 - Samples can be direcly set as references ok 158 - Direct reference assignment works ok 159 - GBZ can represent reference paths without haplotype numbers ok t/38_vg_prune.t ....... 1..21 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 - unfolding with multi-chromosome GBWT produces the correct number of components ok 17 - unfolding with multi-chromosome GBWT produces the correct number of nodes ok 18 - unfolding with multi-chromosome GBWT produces the correct number of edges ok 19 - empty mapping starts from the right node id ok 20 - the first unfolded graph adds the correct number of nodes to the mapping ok 21 - the second unfolded graph adds the correct number of nodes to the mapping ok warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. t/39_vg_inject.t ...... 1..14 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 11 - vg inject does not make an alignment for an umapped read ok 12 - vg inject does not crash on an unmapped read ok 13 - vg inject supports GAF output ok 14 - vg inject produces valid alignments of the read and reference ok warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. 1000 reads correct 1 reads correct 1 reads correct 0 reads correct 0 reads correct 1 reads correct t/40_vg_gamcompare.t .. 1..7 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 are close enough at a long distance with a distance index ok 5 - Reads annotated with leftmost position only are too far apart at a short distance ok 6 - Reads are too far apart at a short distance with a distance index ok 7 - Reads annotated with multiple positions only are close enough at a short distance ok [Viz::init] error: Image would be 86252x88 which is larger than the maximum 32,767 px on a side canvas that Cairo supports for raster images. Use an SVG output, try `odgi viz`, or reduce your input size! t/41_vg_viz.t ......... 1..4 ok 1 - vg viz runs ok 2 - vg viz succeeds when drawing a PNG ok 3 - vg viz actually creates an output PNG ok 4 - vg viz knows when a graph is too big to draw as a PNG 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 graph: valid 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 t/46_vg_minimizer.t ... 1..16 ok 1 - default parameters ok 2 - distance index or --no-dist is required ok 3 - single-threaded construction ok 4 - construction is deterministic ok 5 - syncmer index ok 6 - construction is deterministic ok 7 - minimizer parameters ok 8 - setting -k -w works correctly ok 9 - construction from GBWTGraph ok 10 - construction is deterministic ok 11 - construction from GBZ ok 12 - construction is deterministic ok 13 - construction with payload ok 14 - multiple graphs: first ok 15 - multiple graphs: second ok 16 - 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. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. t/47_vg_dotplot.t ..... 1..1 ok 1 - vg dotplot runs successfully ok [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. warning [vg convert]: currently cannot convert GFA directly to XG; converting through another format [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. warning:[GFAParser] Skipping GFA P line: GFA format error: On pass 1: On line 27: Duplicate path GRCh38.chr1 exists in graph index file ref.fa.fai not found, generating... warning: Thread 2 encountered sequence of length 275, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. alignment: valid graph: valid warning: Thread 34 encountered sequence of length 275, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. alignment: valid graph: valid t/48_vg_convert.t ..... 1..106 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 gfa conversion ok 5 - hash graph conversion looks good ok 6 - packed graph conversion looks good ok 7 - vg conversion looks good ok 8 - gfa 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 - gfa to gfa conversion looks good ok 14 - vg convert gam -> gaf -> gam -> gaf makes same gaf twice ok 15 - vg convert gam -> gaf -> gam -> gaf gives same result multithreaded as with -t 1 ok 16 - vg convert gam -> gaf.gz -> gam -> gaf gives same result multithreaded as with -t 1 ok 17 - vg convert gam -> gaf -> gam produces same gam Paths with snps and indels ok 18 - vg convert gam -> gaf -> gam preserves sequence ok 19 - vg convert gam -> gaf -> gam -> gaf makes same gaf twice in presence of indels and snps ok 20 - vg convert cg-gaf -> gam -> cs-gaf gives expected output (snps converted to matches, insertion converted to Ns) ok 21 - vg convert gam -> gaf -> gam preserves sequences of 1mb1kgp simulated reads ok 22 - vg convert gam -> gaf -> gam ->gaf makes same gaf each time on 1mb1kgp simulated reads ok 23 - split alignment converted using deletions to represent internal offsets ok 24 - vg convert gam -> gaf ->gam -> gaf makes same gaf each time for split alignment ok 25 - convert gam->gaf->gam on softclipped read preserves sequence ok 26 - convert gam->gaf->gam->gaf makes same gaf each time of soft clipped alignment ok 27 - convert gam->gaf->gam on read with floating insertion preserves sequence ok 28 - convert gam->gaf->gam->gaf makes same gaf each time of floating insertion alignment ok 29 - converting gfa and equivalent rgfa produces same output ok 30 - rank-1 rgfa subpath found ok 31 - 2nd column of gfa id translation file contains all rgfa nodes ok 32 - 3rd column of gfa id translation file contains all gfa nodes ok 33 - rgfa output wrote no P-lines ok 34 - rgfa export roundtrips back to normal P-lines ok 35 - GBWTGraph to HashGraph conversion ok 36 - GFA -> GBWTGraph -> HashGraph -> GFA conversion maintains segments ok 37 - GFA -> GBWTGraph -> HashGraph -> GFA conversion maintains walks ok 38 - GBZ to HashGraph conversion ok 39 - GFA -> GBZ -> HashGraph -> GFA conversion maintains segments ok 40 - GBWTGraph to GFA conversion with walks, GBWTGraph algorithm ok 41 - GBWTGraph to GFA conversion with GBWTGraph algorithm creates the correct normalized GFA file ok 42 - GBWTGraph to GFA conversion with walks, vg algorithm ok 43 - GBWTGraph to GFA conversion with vg algorithm creates the correct possibly-unnormalized GFA file ok 44 - GBZ to GFA conversion with walks, GBWTGraph algorithm ok 45 - GBZ to GFA conversion with GBWTGraph algorithm creates the correct normalized GFA file ok 46 - GFA to HashGraph conversion ok 47 - GFA -> HashGraph -> GFA conversion maintains segments, links, walks, and paths ok 48 - GBWTGraph to HashGraph conversion with generic paths ok 49 - GBWTGraph to HashGraph conversion creates the correct generic paths ok 50 - GBWTGraph to HashGraph conversion creates the correct haplotype paths ok 51 - GBZ to HashGraph conversion with generic paths ok 52 - GBZ to HashGraph conversion creates the correct generic paths ok 53 - GBZ to HashGraph conversion creates the correct haplotype paths ok 54 - GBWTGraph to XG conversion with generic paths ok 55 - GBWTGraph to XG conversion creates the correct generic paths ok 56 - GBWTGraph to XG conversion creates the correct haplotype paths ok 57 - GBZ to XG conversion with generic paths ok 58 - GBZ to XG conversion creates the correct generic paths ok 59 - GBZ to XG conversion creates the correct haplotype paths ok 60 - GBZ to XG conversion while dropping haplotypes ok 61 - No haplotypes in the converted graph ok 62 - GBZ to HashGraph conversion while dropping haplotypes ok 63 - No haplotypes in the converted graph ok 64 - GBWTGraph to GFA conversion with paths and walks, GBWTGraph algorithm ok 65 - GBWTGraph to GFA conversion with GBWTGraph algorithm creates the expected normalized GFA file ok 66 - GBWTGraph to GFA conversion with paths and walks, vg algorithm ok 67 - GBWTGraph to GFA conversion with vg algorithm creates the correct possibly-unnormalized GFA file ok 68 - GBWTGraph to HashGraph conversion with paths and walks ok 69 - HashGraph to GFA conversion with paths and walks ok 70 - GBWTGraph to HashGraph to GFA conversion creates the correct possibly-unnormalized GFA file ok 71 - HashGraph to GFA conversion writing walks as paths ok 72 - HashGraph to GFA conversion writing walks as paths produces no walks ok 73 - HashGraph to GFA conversion writing walks as paths produces all expected paths ok 74 - GBZ to GFA conversion with paths and walks, GBWTGraph algorithm ok 75 - GBZ to GFA conversion with GBWTGraph algorithm creates the correct normalized GFA file ok 76 - GBZ to GFA conversion works with multiple threads ok 77 - GBZ to GFA with translation ok 78 - 8 segments ok 79 - GBZ to GFA without translation ok 80 - 9 segments ok 81 - GFA -> GBZ conversion preserves path metadata ok 82 - GFA -> GBZ -> GFA conversion preserves path metadata ok 83 - GFA -> HashGraph conversion preserves path metadata ok 84 - GFA -> HashGraph -> GFA conversion preserves path metadata ok 85 - rGFA -> HashGraph -> GBZ conversion preserves path metadata ok 86 - rGFA -> HashGraph -> GBZ -> GFA conversion preserves path metadata ok 87 - GFA -> HashGraph conversion works with redundant paths ok 88 - GFA -> HashGraph conversion with redundant paths keeps one copy of the redundant path ok 89 - GFA -> HashGraph conversion works with two-part reference path names ok 90 - GFA -> HashGraph conversion with with two-part reference path names gets the right paths ok 91 - No difference roundtripping a GFA if it's loaded as a GFA or HandleGraph warning:[GFAParser] Streaming GFA file references node 6 before it is defined. GFA lines will be buffered in a temporary file. ok 92 - Streaming an unsorted GFA gives same output as sorted ok 93 - Warning given when falling back to temp GFA buffer file ok 94 - Streaming an sorted GFA gives same output as reading from file ok 95 - No warnings given when streamed GFA is sorted ok 96 - Modding GFA directly produces same output as going through convert ok 97 - Modding sorted GFA stream produces same output as going through convert warning:[GFAParser] Streaming GFA file references node 6 before it is defined. GFA lines will be buffered in a temporary file. ok 98 - Modding unsorted GFA stream produces same output as going through convert ok 99 - Warning given when falling back to temp GFA buffer file in mod ok 100 - Modding unsorted GFA file produces same output as going through convert ok 101 - No warnings given when input GFA file is unsorted ok 102 - rGFA handled consistently when streaming as when loaded from file ok 103 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output (GAF check) ok 104 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output (GAM check) ok 105 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output for long node (GAF check) ok 106 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output for long node (GAM check) ok [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. t/49_vg_depth.t ....... 1..6 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 5 - vg depth of paths reports all paths ok 6 - vg depth of paths reports just path with selected prefix ok [IndexRegistry]: Constructing GBZ. Guessing that x.gbwt is Giraffe GBWT Guessing that x.xg is XG Guessing that x.xg is XG [IndexRegistry]: Combining Giraffe GBWT and GBWTGraph into GBZ. Guessing that x.gbwt is Giraffe GBWT Guessing that x.xg is XG Guessing that x.gg is GBWTGraph [IndexRegistry]: Constructing minimizer index. Guessing that x.dist is Giraffe Distance Index Guessing that x.gbwt is Giraffe GBWT Guessing that x.min is Minimizers Guessing that x.xg is XG Guessing that x.gg is GBWTGraph Guessing that x.dist is Giraffe Distance Index Guessing that x.gbwt is Giraffe GBWT Guessing that x.min is Minimizers Guessing that x.xg is XG Guessing that x.gg is GBWTGraph Guessing that x.dist is Giraffe Distance Index Guessing that x.gbwt is Giraffe GBWT Guessing that x.min is Minimizers Guessing that x.xg is XG Guessing that x.gg is GBWTGraph Guessing that x.dist is Giraffe Distance Index Guessing that x.gbwt is Giraffe GBWT Guessing that x.min is Minimizers Guessing that x.xg is XG Guessing that x.gg is GBWTGraph [vg minimizer] warning: --bounded-syncmers is deprecated, use --closed-syncmers instead Guessing that x.gg is GBWTGraph Guessing that x.giraffe.gbz is Giraffe GBZ Guessing that x.gg is GBWTGraph Guessing that x.giraffe.gbz is Giraffe GBZ Guessing that x.gg is GBWTGraph Guessing that x.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. index file x.fa.fai not found, generating... [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Downsampling full GBWT. [IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. [IndexRegistry]: Constructing GBZ. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. [IndexRegistry]: Checking for phasing in VCF(s). Guessing that x.dist is Giraffe Distance Index Guessing that x.min is Minimizers Guessing that x.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). Guessing that x.dist is Giraffe Distance Index Guessing that x.min is Minimizers Guessing that x.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). Guessing that x.dist is Giraffe Distance Index Guessing that x.min is Minimizers Guessing that x.giraffe.gbz is Giraffe GBZ warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning[vg::giraffe]: Finalizing fragment length distribution before reaching maximum sample size mapped 1 reads single ended with 0 pairs of reads left unmapped mean: 0, stdev: 1 [IndexRegistry]: Checking for phasing in VCF(s). Guessing that x.dist is Giraffe Distance Index Guessing that x.min is Minimizers Guessing that x.giraffe.gbz is Giraffe GBZ warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. index file xy.fa.fai not found, generating... [IndexRegistry]: Chunking FASTA(s). [IndexRegistry]: Chunking VCF(s). [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Downsampling full GBWT. [IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. [IndexRegistry]: Constructing GBZ. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg autoindex] Executing command: vg autoindex -p brca -w giraffe -g graphs/cactus-BRCA2.gfa [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing VG graph from GFA input. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Constructing a greedy path cover GBWT [IndexRegistry]: Constructing GBZ using NamedNodeBackTranslation. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. [W::bgzf_read_block] EOF marker is absent. The input may be truncated terminate called after throwing an instance of 'std::runtime_error' what(): [vg::io::MessageIterator] obsolete, invalid, or corrupt input at message 79256662206 group 79256662202 ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" Stack trace (most recent call last): #24 Object "/usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2", at 0xffffffffffffffff, in #23 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583f99a3380, in _start #22 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fe432233e24, in __libc_start_main #21 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fe432233d67, in #20 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583fa1c298f, in vg::subcommand::Subcommand::operator()(int, char**) const | Source "src/subcommand/subcommand.cpp", line 75, in operator() Source "/usr/include/c++/14/bits/std_function.h", line 591, in operator() [0x5583fa1c298f] 588: { 589: if (_M_empty()) 590: __throw_bad_function_call(); > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); 592: } 593: 594: #if __cpp_rtti #19 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583fa12d443, in main_index(int, char**) Source "src/subcommand/index_main.cpp", line 709, in main_index [0x5583fa12d443] #18 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583fa131645, in std::tuple >, std::unique_ptr > > vg::io::VPKG::try_load_first(std::__cxx11::basic_string, std::allocator > const&) Source "./include/vg/io/vpkg.hpp", line 112, in try_load_first [0x5583fa131645] #17 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583fa1313ee, in std::tuple >, std::unique_ptr > > vg::io::VPKG::try_load_first(std::istream&, std::__cxx11::basic_string, std::allocator > const&) Source "./include/vg/io/vpkg.hpp", line 64, in try_load_first [0x5583fa1313ee] #16 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583f9fdcfde, in vg::io::VPKG::with_putback(std::istream&, std::function const&) | Source "./include/vg/io/vpkg.hpp", line 595, in operator() Source "/usr/include/c++/14/bits/std_function.h", line 591, in with_putback [0x5583f9fdcfde] 588: { 589: if (_M_empty()) 590: __throw_bad_function_call(); > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); 592: } 593: 594: #if __cpp_rtti #15 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583fa131a99, in std::_Function_handler(std::istream&, std::__cxx11::basic_string, std::allocator > const&)::{lambda(std::istream&)#1}>::_M_invoke(std::_Any_data const&, std::istream&) | Source "/usr/include/c++/14/bits/std_function.h", line 290, in __invoke_r(std::istream&, const std::string&)::&, std::basic_istream >&> | 288: _M_invoke(const _Any_data& __functor, _ArgTypes&&... __args) | 289: { | > 290: return std::__invoke_r<_Res>(*_Base::_M_get_pointer(__functor), | 291: std::forward<_ArgTypes>(__args)...); | 292: } | Source "/usr/include/c++/14/bits/invoke.h", line 150, in __invoke_impl(std::istream&, const std::string&)::&, std::basic_istream >&> | 148: using __type = typename __result::type; | 149: using __tag = typename __result::__invoke_type; | > 150: std::__invoke_impl<__type>(__tag{}, std::forward<_Callable>(__fn), | 151: std::forward<_Args>(__args)...); | 152: } | Source "/usr/include/c++/14/bits/invoke.h", line 61, in operator() | 59: constexpr _Res | 60: __invoke_impl(__invoke_other, _Fn&& __f, _Args&&... __args) | > 61: { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); } | 62: | 63: template | Source "./include/vg/io/vpkg.hpp", line 77, in try_load_first_encapsulated | Source "./include/vg/io/vpkg.hpp", line 401, in try_load_first_encapsulated Source "./include/vg/io/vpkg.hpp", line 416, in _M_invoke [0x5583fa131a99] #14 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583f9fe0320, in std::unique_ptr > vg::io::VPKG::try_load_encapsulated(vg::io::MessageIterator&) | Source "./include/vg/io/vpkg.hpp", line 565, in operator() Source "/usr/include/c++/14/bits/std_function.h", line 591, in try_load_encapsulated [0x5583f9fe0320] 588: { 589: if (_M_empty()) 590: __throw_bad_function_call(); > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); 592: } 593: 594: #if __cpp_rtti #13 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583fa9b751b, in std::_Function_handler, std::allocator > const&)> const&)> const&), vg::io::register_loader_saver_hash_graph()::{lambda(std::function, std::allocator > const&)> const&)> const&)#1}>::_M_invoke(std::_Any_data const&, std::function, std::allocator > const&)> const&)> const&) | Source "/usr/include/c++/14/bits/std_function.h", line 290, in __invoke_r&, const std::function, std::allocator >&)>&)>&> | 288: _M_invoke(const _Any_data& __functor, _ArgTypes&&... __args) | 289: { | > 290: return std::__invoke_r<_Res>(*_Base::_M_get_pointer(__functor), | 291: std::forward<_ArgTypes>(__args)...); | 292: } | Source "/usr/include/c++/14/bits/invoke.h", line 138, in __invoke_impl&, const std::function, std::allocator >&)>&)>&> | 136: #endif | 137: using __tag = typename __result::__invoke_type; | > 138: return std::__invoke_impl<__type>(__tag{}, std::forward<_Callable>(__fn), | 139: std::forward<_Args>(__args)...); | 140: } | Source "/usr/include/c++/14/bits/invoke.h", line 61, in operator() | 59: constexpr _Res | 60: __invoke_impl(__invoke_other, _Fn&& __f, _Args&&... __args) | > 61: { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); } | 62: | 63: template Source "src/io/register_loader_saver_hash_graph.cpp", line 58, in _M_invoke [0x5583fa9b751b] #12 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583fa9952bd, in vg::io::load_proto_to_graph(handlegraph::MutablePathMutableHandleGraph*, std::function, std::allocator > const&)> const&)> const&) Source "src/io/load_proto_to_graph.cpp", line 35, in load_proto_to_graph [0x5583fa9952bd] #11 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583fa994c1f, in vg::io::load_proto_to_graph(handlegraph::MutablePathMutableHandleGraph*, std::function const&)> const&) | Source "src/io/load_proto_to_graph.cpp", line 76, in operator() Source "/usr/include/c++/14/bits/std_function.h", line 591, in load_proto_to_graph [0x5583fa994c1f] 588: { 589: if (_M_empty()) 590: __throw_bad_function_call(); > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); 592: } 593: 594: #if __cpp_rtti #10 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583fa992605, in std::_Function_handler const&), vg::io::load_proto_to_graph(handlegraph::MutablePathMutableHandleGraph*, std::function, std::allocator > const&)> const&)> const&)::{lambda(std::function const&)#1}>::_M_invoke(std::_Any_data const&, std::function const&) | Source "/usr/include/c++/14/bits/std_function.h", line 290, in __invoke_r&)>&, const std::function&> | 288: _M_invoke(const _Any_data& __functor, _ArgTypes&&... __args) | 289: { | > 290: return std::__invoke_r<_Res>(*_Base::_M_get_pointer(__functor), | 291: std::forward<_ArgTypes>(__args)...); | 292: } | Source "/usr/include/c++/14/bits/invoke.h", line 150, in __invoke_impl&)>&, const std::function&> | 148: using __type = typename __result::type; | 149: using __tag = typename __result::__invoke_type; | > 150: std::__invoke_impl<__type>(__tag{}, std::forward<_Callable>(__fn), | 151: std::forward<_Args>(__args)...); | 152: } | Source "/usr/include/c++/14/bits/invoke.h", line 61, in operator() | 59: constexpr _Res | 60: __invoke_impl(__invoke_other, _Fn&& __f, _Args&&... __args) | > 61: { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); } | 62: | 63: template | Source "src/io/load_proto_to_graph.cpp", line 37, in operator() Source "/usr/include/c++/14/bits/std_function.h", line 591, in _M_invoke [0x5583fa992605] 588: { 589: if (_M_empty()) 590: __throw_bad_function_call(); > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); 592: } 593: 594: #if __cpp_rtti #9 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583f9fdc394, in std::_Function_handler, std::allocator > const&)> const&), vg::io::VPKG::try_load_encapsulated(vg::io::MessageIterator&)::{lambda(std::function, std::allocator > const&)> const&)#1}>::_M_invoke(std::_Any_data const&, std::function, std::allocator > const&)> const&) | Source "/usr/include/c++/14/bits/std_function.h", line 290, in __invoke_r(vg::io::MessageIterator&)::&, const std::function, std::allocator >&)>&> | 288: _M_invoke(const _Any_data& __functor, _ArgTypes&&... __args) | 289: { | > 290: return std::__invoke_r<_Res>(*_Base::_M_get_pointer(__functor), | 291: std::forward<_ArgTypes>(__args)...); | 292: } | Source "/usr/include/c++/14/bits/invoke.h", line 150, in __invoke_impl(vg::io::MessageIterator&)::&, const std::function, std::allocator >&)>&> | 148: using __type = typename __result::type; | 149: using __tag = typename __result::__invoke_type; | > 150: std::__invoke_impl<__type>(__tag{}, std::forward<_Callable>(__fn), | 151: std::forward<_Args>(__args)...); | 152: } | Source "/usr/include/c++/14/bits/invoke.h", line 61, in operator() | 59: constexpr _Res | 60: __invoke_impl(__invoke_other, _Fn&& __f, _Args&&... __args) | > 61: { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); } | 62: | 63: template Source "./include/vg/io/vpkg.hpp", line 571, in _M_invoke [0x5583f9fdc394] #8 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583fae06005, in vg::io::MessageIterator::operator++() Source "./deps/libvgio/src/message_iterator.cpp", line 361, in operator++ [0x5583fae06005] #7 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583f995bd4e, in vg::io::MessageIterator::handle(bool, long, long) [clone .cold] Source "./deps/libvgio/src/message_iterator.cpp", line 472, in handle [0x5583f995bd4e] #6 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.33", at 0x7fe4324b3287, in __cxa_throw #5 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.33", at 0x7fe4324a15e8, in std::terminate() #4 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.33", at 0x7fe4324b3009, in #3 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.33", at 0x7fe4324a1a3c, in #2 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fe4322324ef, in abort #1 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fe432249c41, in raise #0 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fe43229dc8c, in ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ [vg autoindex] Executing command: vg autoindex -p 1mb1kgp -w giraffe -P VG w/ Variant Paths:1mb1kgp.vg -P Giraffe Distance Index:1mb1kgp.dist -r 1mb1kgp/z.fa -v 1mb1kgp/z.vcf.gz [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Stripping allele paths from VG. [W::bgzf_read_block] EOF marker is absent. The input may be truncated terminate called after throwing an instance of 'std::runtime_error' what(): [vg::io::MessageIterator] obsolete, invalid, or corrupt input at message 79256662206 group 79256662202 ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" Stack trace (most recent call last) in thread 3281365: #23 Object "/usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2", at 0xffffffffffffffff, in #22 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fba0a91a677, in #21 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fba0a89bf51, in #20 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.33", at 0x7fba0aae0ea3, in #19 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x562431dd5f43, in std::thread::_State_impl > >::_M_run() | Source "/usr/include/c++/14/bits/std_thread.h", line 253, in operator() | 252: void | > 253: _M_run() { _M_func(); } | 254: }; | Source "/usr/include/c++/14/bits/std_thread.h", line 308, in _M_invoke<0> | 306: using _Indices | 307: = typename _Build_index_tuple::value>::__type; | > 308: return _M_invoke(_Indices()); | 309: } | 310: }; | Source "/usr/include/c++/14/bits/std_thread.h", line 301, in __invoke > | 299: typename __result<_Tuple>::type | 300: _M_invoke(_Index_tuple<_Ind...>) | > 301: { return std::__invoke(std::get<_Ind>(std::move(_M_t))...); } | 302: | 303: typename __result<_Tuple>::type | Source "/usr/include/c++/14/bits/invoke.h", line 96, in __invoke_impl > | 94: using __type = typename __result::type; | 95: using __tag = typename __result::__invoke_type; | > 96: return std::__invoke_impl<__type>(__tag{}, std::forward<_Callable>(__fn), | 97: std::forward<_Args>(__args)...); | 98: } | Source "/usr/include/c++/14/bits/invoke.h", line 61, in operator() | 59: constexpr _Res | 60: __invoke_impl(__invoke_other, _Fn&& __f, _Args&&... __args) | > 61: { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); } | 62: | 63: template | Source "src/job_schedule.cpp", line 77, in operator() Source "/usr/include/c++/14/bits/std_function.h", line 591, in _M_run [0x562431dd5f43] 588: { 589: if (_M_empty()) 590: __throw_bad_function_call(); > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); 592: } 593: 594: #if __cpp_rtti #18 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x562431d9013a, in vg::VGIndexes::get_vg_index_registry()::{lambda(std::vector > const&, vg::IndexingPlan const*, std::set, std::allocator >, std::less, std::allocator > >, std::allocator, std::allocator > > > const&)#1}::operator()(std::vector > const&, vg::IndexingPlan const*, std::set, std::allocator >, std::less, std::allocator > >, std::allocator, std::allocator > > > const&) const::{lambda(long)#1}::operator()(long) const Source "src/index_registry.cpp", line 1752, in operator() [0x562431d9013a] #17 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x562431dbe043, in std::unique_ptr > vg::io::VPKG::load_one(std::istream&, std::__cxx11::basic_string, std::allocator > const&) | Source "./include/vg/io/vpkg.hpp", line 187, in try_load_one Source "./include/vg/io/vpkg.hpp", line 135, in load_one [0x562431dbe043] #16 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5624318e7fde, in vg::io::VPKG::with_putback(std::istream&, std::function const&) | Source "./include/vg/io/vpkg.hpp", line 595, in operator() Source "/usr/include/c++/14/bits/std_function.h", line 591, in with_putback [0x5624318e7fde] 588: { 589: if (_M_empty()) 590: __throw_bad_function_call(); > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); 592: } 593: 594: #if __cpp_rtti #15 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x562431922357, in std::_Function_handler(std::istream&, std::__cxx11::basic_string, std::allocator > const&)::{lambda(std::istream&)#1}>::_M_invoke(std::_Any_data const&, std::istream&) | Source "/usr/include/c++/14/bits/std_function.h", line 290, in __invoke_r(std::istream&, const std::string&)::&, std::basic_istream >&> | 288: _M_invoke(const _Any_data& __functor, _ArgTypes&&... __args) | 289: { | > 290: return std::__invoke_r<_Res>(*_Base::_M_get_pointer(__functor), | 291: std::forward<_ArgTypes>(__args)...); | 292: } | Source "/usr/include/c++/14/bits/invoke.h", line 150, in __invoke_impl(std::istream&, const std::string&)::&, std::basic_istream >&> | 148: using __type = typename __result::type; | 149: using __tag = typename __result::__invoke_type; | > 150: std::__invoke_impl<__type>(__tag{}, std::forward<_Callable>(__fn), | 151: std::forward<_Args>(__args)...); | 152: } | Source "/usr/include/c++/14/bits/invoke.h", line 61, in operator() | 59: constexpr _Res | 60: __invoke_impl(__invoke_other, _Fn&& __f, _Args&&... __args) | > 61: { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); } | 62: | 63: template | Source "./include/vg/io/vpkg.hpp", line 135, in operator() | Source "./include/vg/io/vpkg.hpp", line 141, in try_load_encapsulated | Source "./include/vg/io/vpkg.hpp", line 482, in with_putback | Source "./include/vg/io/vpkg.hpp", line 595, in operator() Source "/usr/include/c++/14/bits/std_function.h", line 591, in _M_invoke [0x562431922357] 588: { 589: if (_M_empty()) 590: __throw_bad_function_call(); > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); 592: } 593: 594: #if __cpp_rtti #14 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5624319246ff, in std::_Function_handler(std::istream&)::{lambda(std::istream&)#1}>::_M_invoke(std::_Any_data const&, std::istream&) | Source "/usr/include/c++/14/bits/std_function.h", line 290, in __invoke_r(std::istream&)::&, std::basic_istream >&> | 288: _M_invoke(const _Any_data& __functor, _ArgTypes&&... __args) | 289: { | > 290: return std::__invoke_r<_Res>(*_Base::_M_get_pointer(__functor), | 291: std::forward<_ArgTypes>(__args)...); | 292: } | Source "/usr/include/c++/14/bits/invoke.h", line 150, in __invoke_impl(std::istream&)::&, std::basic_istream >&> | 148: using __type = typename __result::type; | 149: using __tag = typename __result::__invoke_type; | > 150: std::__invoke_impl<__type>(__tag{}, std::forward<_Callable>(__fn), | 151: std::forward<_Args>(__args)...); | 152: } | Source "/usr/include/c++/14/bits/invoke.h", line 61, in operator() | 59: constexpr _Res | 60: __invoke_impl(__invoke_other, _Fn&& __f, _Args&&... __args) | > 61: { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); } | 62: | 63: template | Source "./include/vg/io/vpkg.hpp", line 526, in try_load_encapsulated | Source "./include/vg/io/vpkg.hpp", line 565, in operator() Source "/usr/include/c++/14/bits/std_function.h", line 591, in _M_invoke [0x5624319246ff] 588: { 589: if (_M_empty()) 590: __throw_bad_function_call(); > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); 592: } 593: 594: #if __cpp_rtti #13 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5624322c251b, in std::_Function_handler, std::allocator > const&)> const&)> const&), vg::io::register_loader_saver_hash_graph()::{lambda(std::function, std::allocator > const&)> const&)> const&)#1}>::_M_invoke(std::_Any_data const&, std::function, std::allocator > const&)> const&)> const&) | Source "/usr/include/c++/14/bits/std_function.h", line 290, in __invoke_r&, const std::function, std::allocator >&)>&)>&> | 288: _M_invoke(const _Any_data& __functor, _ArgTypes&&... __args) | 289: { | > 290: return std::__invoke_r<_Res>(*_Base::_M_get_pointer(__functor), | 291: std::forward<_ArgTypes>(__args)...); | 292: } | Source "/usr/include/c++/14/bits/invoke.h", line 138, in __invoke_impl&, const std::function, std::allocator >&)>&)>&> | 136: #endif | 137: using __tag = typename __result::__invoke_type; | > 138: return std::__invoke_impl<__type>(__tag{}, std::forward<_Callable>(__fn), | 139: std::forward<_Args>(__args)...); | 140: } | Source "/usr/include/c++/14/bits/invoke.h", line 61, in operator() | 59: constexpr _Res | 60: __invoke_impl(__invoke_other, _Fn&& __f, _Args&&... __args) | > 61: { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); } | 62: | 63: template Source "src/io/register_loader_saver_hash_graph.cpp", line 58, in _M_invoke [0x5624322c251b] #12 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5624322a02bd, in vg::io::load_proto_to_graph(handlegraph::MutablePathMutableHandleGraph*, std::function, std::allocator > const&)> const&)> const&) Source "src/io/load_proto_to_graph.cpp", line 35, in load_proto_to_graph [0x5624322a02bd] #11 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x56243229fc1f, in vg::io::load_proto_to_graph(handlegraph::MutablePathMutableHandleGraph*, std::function const&)> const&) | Source "src/io/load_proto_to_graph.cpp", line 76, in operator() Source "/usr/include/c++/14/bits/std_function.h", line 591, in load_proto_to_graph [0x56243229fc1f] 588: { 589: if (_M_empty()) 590: __throw_bad_function_call(); > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); 592: } 593: 594: #if __cpp_rtti #10 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x56243229d605, in std::_Function_handler const&), vg::io::load_proto_to_graph(handlegraph::MutablePathMutableHandleGraph*, std::function, std::allocator > const&)> const&)> const&)::{lambda(std::function const&)#1}>::_M_invoke(std::_Any_data const&, std::function const&) | Source "/usr/include/c++/14/bits/std_function.h", line 290, in __invoke_r&)>&, const std::function&> | 288: _M_invoke(const _Any_data& __functor, _ArgTypes&&... __args) | 289: { | > 290: return std::__invoke_r<_Res>(*_Base::_M_get_pointer(__functor), | 291: std::forward<_ArgTypes>(__args)...); | 292: } | Source "/usr/include/c++/14/bits/invoke.h", line 150, in __invoke_impl&)>&, const std::function&> | 148: using __type = typename __result::type; | 149: using __tag = typename __result::__invoke_type; | > 150: std::__invoke_impl<__type>(__tag{}, std::forward<_Callable>(__fn), | 151: std::forward<_Args>(__args)...); | 152: } | Source "/usr/include/c++/14/bits/invoke.h", line 61, in operator() | 59: constexpr _Res | 60: __invoke_impl(__invoke_other, _Fn&& __f, _Args&&... __args) | > 61: { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); } | 62: | 63: template | Source "src/io/load_proto_to_graph.cpp", line 37, in operator() Source "/usr/include/c++/14/bits/std_function.h", line 591, in _M_invoke [0x56243229d605] 588: { 589: if (_M_empty()) 590: __throw_bad_function_call(); > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); 592: } 593: 594: #if __cpp_rtti #9 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5624319220a4, in std::_Function_handler, std::allocator > const&)> const&), vg::io::VPKG::try_load_encapsulated(vg::io::MessageIterator&)::{lambda(std::function, std::allocator > const&)> const&)#1}>::_M_invoke(std::_Any_data const&, std::function, std::allocator > const&)> const&) | Source "/usr/include/c++/14/bits/std_function.h", line 290, in __invoke_r(vg::io::MessageIterator&)::&, const std::function, std::allocator >&)>&> | 288: _M_invoke(const _Any_data& __functor, _ArgTypes&&... __args) | 289: { | > 290: return std::__invoke_r<_Res>(*_Base::_M_get_pointer(__functor), | 291: std::forward<_ArgTypes>(__args)...); | 292: } | Source "/usr/include/c++/14/bits/invoke.h", line 150, in __invoke_impl(vg::io::MessageIterator&)::&, const std::function, std::allocator >&)>&> | 148: using __type = typename __result::type; | 149: using __tag = typename __result::__invoke_type; | > 150: std::__invoke_impl<__type>(__tag{}, std::forward<_Callable>(__fn), | 151: std::forward<_Args>(__args)...); | 152: } | Source "/usr/include/c++/14/bits/invoke.h", line 61, in operator() | 59: constexpr _Res | 60: __invoke_impl(__invoke_other, _Fn&& __f, _Args&&... __args) | > 61: { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); } | 62: | 63: template Source "./include/vg/io/vpkg.hpp", line 571, in _M_invoke [0x5624319220a4] #8 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x562432711005, in vg::io::MessageIterator::operator++() Source "./deps/libvgio/src/message_iterator.cpp", line 361, in operator++ [0x562432711005] #7 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x562431266d4e, in vg::io::MessageIterator::handle(bool, long, long) [clone .cold] Source "./deps/libvgio/src/message_iterator.cpp", line 472, in handle [0x562431266d4e] #6 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.33", at 0x7fba0aab3287, in __cxa_throw #5 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.33", at 0x7fba0aaa15e8, in std::terminate() #4 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.33", at 0x7fba0aab3009, in #3 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.33", at 0x7fba0aaa1a3c, in #2 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fba0a8324ef, in abort #1 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fba0a849c41, in raise #0 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fba0a89dc8c, in ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error:[vg giraffe] Couldn't open GBZ file 1mb1kgp.giraffe.gbz t/50_vg_giraffe.t ..... 1..50 ok 1 - a read can be mapped with xg + gbwt + min + dist specified without crashing ok 2 - a read can be mapped with gbz + min + dist specified without crashing ok 3 - a read can be mapped with gg + gbwt + min + dist specified without crashing ok 4 - a read can be mapped with the minimizer index being regenerated ok 5 - a read can be mapped with the indexes being inferred by name ok 6 - Mapping logs runtime per read ok 7 - Mapping produces the correct score ok 8 - a read can be mapped with the fast preset ok 9 - a read can be mapped with the default preset ok 10 - Mapping without a full length bonus produces the correct score ok 11 - a read can be mapped with syncmer indexes without crashing ok 12 - a read can be mapped when the distance index is not writable ok 13 - a read which softclips does not appear to loop ok 14 - a read can be mapped with just FASTA and VCF without crashing ok 15 - mapping with just a FASTA and a VCF produced JSON-able alignments ok 16 - mapping to manually-generated indexes and automatically-generated indexes is the same ok 17 - mapping with syncmers produces the same alignment as mapping with minimizers ok 18 - unpaired reads lack cross-references ok 19 - paired reads have cross-references ok 20 - surjection of paired reads to SAM yields correct positions ok 21 - surjection of paired reads to SAM yields correct pair partner positions ok 22 - surjection of paired reads to SAM yields properly matched QNAMEs ok 23 - surjection of paired reads to SAM produces correct pair partner contigs ok 24 - surjection of paired reads to SAM produces correct flags ok 25 - surjection of unpaired reads to SAM yields correct positions ok 26 - surjection of unpaired reads to SAM yields correct pair partner positions ok 27 - surjection of unpaired reads to SAM yields distinct QNAMEs ok 28 - surjection of unpaired reads to SAM produces absent partner contigs ok 29 - surjection of unpaired reads to SAM produces correct flags ok 30 - surjecting with a sequence dictionary in non-sorted order produces headers in non-sorted order ok 31 - surjecting with a sequence dictionary in sorted order produces headers in sorted order ok 32 - paired reads are evenly split between equivalent mappings ok 33 - unpaired reads are evenly split between equivalent mappings ok 34 - provenance tracking succeeds for unpaired reads ok 35 - correctness tracking succeeds for unpaired reads ok 36 - unpaired reads are annotated with minimizer coverage ok 37 - provenance tracking succeeds for paired reads ok 38 - correctness tracking succeeds for paired reads ok 39 - paired reads are annotated with minimizer coverage ok 40 - paired reads all have nonzero correct minimizer coverage ok 41 - vg giraffe can map to BAM using a GBZ alone ok 42 - GBZ-based BAM contains the expected number of reads ok 43 - Mapping reads to named coordinates on a nontrivial graph without walks succeeds ok 44 - Reads are all mapped ok 45 - GFA segment names are all set ok 46 - Mapping reads as GAF to named coordinates on a nontrivial graph without walks succeeds ok 47 - Mapping reads as named GAF uses the same names as named GAM not ok 48 - A long read can be correctly aligned # got: '' # expected: '7999' not ok 49 - A long read has the correct edits found # got: '0' # expected: '2' not ok 50 - Long read minimizer set is correctly restricted # got: '0' # expected: '1' Failed 3/50 subtests [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. t/51_vg_combine.t ..... 1..10 ok 1 - combined graph as correct total nodes ok 2 - combined graph as correct total edges ok 3 - combined graph has same input path ok 4 - combined handle graph as correct total nodes ok 5 - combined handle graph as correct total edges ok 6 - combined handle graph has same input path ok 7 - path combined graph as correct total nodes ok 8 - path combined path graph as correct total edges ok 9 - path combined graph as correct number of paths ok 10 - combined path has correct size ok rm: cannot remove 'auto.*': No such file or directory [vg autoindex] Executing command: vg autoindex -p auto -w map -r tiny/tiny.fa -v tiny/tiny.vcf.gz --force-unphased [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Pruning complex regions of VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w map -r small/x.fa -v small/x.vcf.gz -r small/y.fa -v small/y.vcf.gz [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. index file small/y.fa.fai not found, generating... [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Pruning complex regions of VG to prepare for GCSA indexing with GBWT unfolding. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w map -r small/xy.fa -v small/xy2.vcf.gz [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Chunking FASTA(s). [IndexRegistry]: Chunking VCF(s). [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Pruning complex regions of VG to prepare for GCSA indexing with GBWT unfolding. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -w rpvg -r tiny/tiny.fa -v tiny/tiny.vcf.gz -x tiny/tiny.gtf [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from spliced VG graph and phased VCF input. [IndexRegistry]: Stripping allele paths from spliced VG. [IndexRegistry]: Constructing haplotype-transcript GBWT and finishing spliced VG. [IndexRegistry]: Joining transcript origin table. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing with GBWT unfolding. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - [vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -r tiny/tiny.fa -v tiny/tiny.vcf.gz -x tiny/tiny.gtf --force-unphased [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. [IndexRegistry]: Finishing spliced VG. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - [vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -r tiny/tiny.fa -x tiny/tiny.gtf [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing spliced VG graph from FASTA input. [IndexRegistry]: Finishing spliced VG. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - [vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -w rpvg -r small/x.fa -r small/y.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/x.gtf -x small/y.gtf [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from spliced VG graph and phased VCF input. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Stripping allele paths from spliced VG. [IndexRegistry]: Constructing haplotype-transcript GBWT and finishing spliced VG. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Joining transcript origin table. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing with GBWT unfolding. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -r small/x.fa -r small/y.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/x.gtf -x small/y.gtf --force-unphased [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. [IndexRegistry]: Finishing spliced VG. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - [vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -w rpvg -r small/x.fa -r small/y.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/xy.gtf [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Chunking FASTA(s). [IndexRegistry]: Chunking VCF(s). [IndexRegistry]: Chunking GTF/GFF(s). [IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from spliced VG graph and phased VCF input. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Stripping allele paths from spliced VG. [IndexRegistry]: Constructing haplotype-transcript GBWT and finishing spliced VG. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Joining transcript origin table. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing with GBWT unfolding. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -w rpvg -r small/xy.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/xy.gtf [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Chunking FASTA(s). [IndexRegistry]: Chunking VCF(s). [IndexRegistry]: Chunking GTF/GFF(s). [IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from spliced VG graph and phased VCF input. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Stripping allele paths from spliced VG. [IndexRegistry]: Constructing haplotype-transcript GBWT and finishing spliced VG. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Joining transcript origin table. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing with GBWT unfolding. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -g graphs/gfa_with_w_lines.gfa -x graphs/gfa_with_w_lines.gtf [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing a GBZ from GFA input. [IndexRegistry]: Adding splice junctions to GBZ-format graph. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - [vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -g graphs/gfa_with_w_lines.gfa -x graphs/gfa_with_w_lines.gtf -H graphs/gfa_with_w_lines_haplo.gtf [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing a GBZ from GFA input. [IndexRegistry]: Adding splice junctions to GBZ-format graph. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - [vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 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 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. [vg autoindex] Executing command: vg autoindex -p auto -w rpvg -w mpmap -g graphs/gfa_with_w_lines.gfa -x graphs/gfa_with_w_lines.gtf [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing a GBZ from GFA input. [IndexRegistry]: Constructing haplotype-transcript GBWT and spliced graph from GBZ-format graph. [IndexRegistry]: Joining transcript origin table. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w rpvg -w mpmap -g graphs/gfa_with_w_lines.gfa -x graphs/gfa_with_w_lines.gtf -H graphs/gfa_with_w_lines_haplo.gtf [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing a GBZ from GFA input. [IndexRegistry]: Constructing haplotype-transcript GBWT and spliced graph from GBZ-format graph. [IndexRegistry]: Joining transcript origin table. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w giraffe -r tiny/tiny.fa -v tiny/tiny.vcf.gz [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Downsampling full GBWT. [IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. [IndexRegistry]: Constructing GBZ. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. [vg autoindex] Executing command: vg autoindex -p auto -w giraffe -g graphs/gfa_with_w_lines.gfa [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing a GBZ from GFA input. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. warning [vg convert]: currently cannot convert GFA directly to XG; converting through another format [vg autoindex] Executing command: vg autoindex -p auto -w giraffe -g graphs/named_with_walk.gfa [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing a GBZ from GFA input. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. [vg autoindex] Executing command: vg autoindex -p auto -w giraffe -g graphs/named.gfa [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing VG graph from GFA input. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Constructing a greedy path cover GBWT [IndexRegistry]: Constructing GBZ using NamedNodeBackTranslation. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. t/52_vg_autoindex.t ... 1..49 ok 1 - autoindexing successfully completes indexing for vg map with basic input ok 2 - autoindexing makes 3 outputs for vg map ok 3 - autoindexing makes an XG for vg map ok 4 - autoindexing makes a GCSA2/LCP pair for vg map ok 5 - basic autoindexing results can be used by vg map ok 6 - autoindexing successfully completes indexing for vg map with chunked input ok 7 - chunked autoindexing results can be used by vg map ok 8 - autoindexing successfully completes indexing for vg map with phased input ok 9 - phased autoindexing results can be used by vg map ok 10 - autoindexing successfully completes indexing for vg mpmap with unchunked input ok 11 - autoindexing creates 6 files for mpmap/rpvg ok 12 - basic autoindexing results can be used by vg mpmap ok 13 - haplotype transcript GBWT made by autoindex is valid ok 14 - transcript origin table has expected number of rows ok 15 - autoindexing successfully completes indexing for vg mpmap with unchunked, unphased input ok 16 - autoindexing creates 4 files for mpmap/rpvg ok 17 - basic unphased autoindexing results can be used by vg mpmap ok 18 - autoindexing successfully completes indexing for vg mpmap without variants ok 19 - autoindexing creates 4 files for mpmap without variants ok 20 - autoindexing results with no variants can be used by vg mpmap ok 21 - autoindexing successfully completes indexing for vg mpmap with chunked input ok 22 - autoindexing creates 6 files for mpmap/rpvg with chunked input ok 23 - autoindexing successfully completes indexing for vg mpmap with unphased chunked input ok 24 - autoindexing creates 4 files for mpmap/rpvg with chunked input ok 25 - autoindexing results with chunked unphased input can be used by vg mpmap ok 26 - autoindexing successfully completes indexing for vg mpmap with partially chunked input ok 27 - autoindexing successfully completes indexing for vg mpmap with another partially chunked input ok 28 - autoindexing successfully completes indexing for vg mpmap with GFA input ok 29 - autoindexing results with GFA input can be used by vg mpmap ok 30 - autoindexing successfully completes indexing for vg mpmap with GFA input and a haplotype GTF ok 31 - autoindexing results with GFA input and a haplotype GTF can be used by vg mpmap ok 32 - autoindexing successfully completes indexing for vg mpmap and rpvg with GFA input ok 33 - autoindexing successfully completes indexing for vg mpmap and rpvg with GFA input and a haplotype GTF ok 34 - autoindexing successfully completes indexing for vg giraffe with unchunked input ok 35 - autoindexing creates 3 inputs for vg giraffe ok 36 - basic autoindexing results can be used by vg giraffe ok 37 - autoindexing successfully completes indexing for vg giraffe with GFA input with W-lines ok 38 - autoindexing creates 3 inputs for vg giraffe from GFA input ok 39 - GFA autoindexing results can be used by vg giraffe ok 40 - autoindexing successfully completes on a GFA with named segments and W-lines ok 41 - GFA segment names are available in output GAM when a walk exists ok 42 - autoindexing successfully completes on a GFA with named segments and no W-lines ok 43 - GFA segment names are available in output GAM when no walks exist ok 44 - Running out of room during k-mer enumeration triggers a rewind ok 45 - Indexing is successful after rewinding from k-mer generation ok 46 - Running out of room during GCSA2 indexing triggers a rewind ok 47 - Indexing is successful after rewinding from GCSA2 indexing ok 48 - Running out of memory during GCSA2 indexing triggers a rewind ok 49 - Indexing is successful after rewinding from GCSA2 indexing 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: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 1014 [algorithms::normalize] normalized in 0 steps graph: valid graph: valid graph: valid graph: valid graph: valid graph: valid t/53_clip.t ........... 1..17 ok 1 - clipped graph is valid ok 2 - every step in clipped graph belongs to reference path ok 3 - clipped graph has same length as ref path ok 4 - clipped graph is valid ok 5 - Just one node filtered ok 6 - clipped graph is valid ok 7 - Just one edge filtered ok 8 - clipped graph is valid ok 9 - Just one node filtered ok 10 - clipped graph is valid ok 11 - clipping bad region changes nothing ok 12 - clipped graph is valid ok 13 - Just one node filtered ok 14 - stub clipping removed all stubs ok 15 - region clipping filtered out only 2 / 4 stub nodes ok 16 - Correct head after path stubbification ok 17 - Correct tail after path stubbification ok t/54_vg_haplotypes.t .. 1..21 ok 1 - generating haplotype information ok 2 - sampling from existing haplotype information ok 3 - 1 generated + 2 reference samples ok 4 - 2 contigs ok 5 - 4 generated + 2 reference haplotypes ok 6 - sampling the haplotypes directly ok 7 - the outputs are identical ok 8 - sampling without adding reference ok 9 - 1 sample ok 10 - 2 contigs ok 11 - 4 haplotypes ok 12 - diploid sampling ok 13 - 1 generated + 2 reference samples ok 14 - 2 contigs ok 15 - 2 generated + 2 reference haplotypes ok 16 - diploid sampling using a preset ok 17 - the outputs are identical ok 18 - Giraffe integration with a guessed output name ok 19 - the sampled graph is identical to a manually sampled one ok 20 - Giraffe integration with a specified output name ok 21 - the sampled graphs are identical ok Test Summary Report ------------------- t/02_vg_construct.t (Wstat: 0 Tests: 30 Failed: 1) Failed test: 7 t/50_vg_giraffe.t (Wstat: 0 Tests: 50 Failed: 3) Failed tests: 48-50 Files=53, Tests=1138, 1018 wallclock secs ( 0.56 usr 0.13 sys + 6099.17 cusr 1025.03 csys = 7124.89 CPU) Result: FAIL Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Address sizes: 40 bits physical, 48 bits virtual Byte Order: Little Endian CPU(s): 42 On-line CPU(s) list: 0-41 Vendor ID: GenuineIntel Model name: Intel Core Processor (Haswell) CPU family: 6 Model: 60 Thread(s) per core: 2 Core(s) per socket: 1 Socket(s): 21 Stepping: 1 BogoMIPS: 4788.90 Virtualization: VT-x Hypervisor vendor: Microsoft Virtualization type: full L1d cache: 672 KiB (21 instances) L1i cache: 672 KiB (21 instances) L2 cache: 84 MiB (21 instances) NUMA node(s): 1 NUMA node0 CPU(s): 0-41 Vulnerability Gather data sampling: Not affected Vulnerability Itlb multihit: KVM: Mitigation: VMX disabled Vulnerability L1tf: Mitigation; PTE Inversion; VMX conditional cache flushes, SMT vulnerable Vulnerability Mds: Mitigation; Clear CPU buffers; SMT Host state unknown Vulnerability Meltdown: Mitigation; PTI Vulnerability Mmio stale data: Unknown: No mitigations Vulnerability Reg file data sampling: Not affected Vulnerability Retbleed: Not affected Vulnerability Spec rstack overflow: Not affected Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl Vulnerability Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization Vulnerability Spectre v2: Mitigation; Retpolines; IBPB conditional; IBRS_FW; STIBP conditional; RSB filling; PBRSB-eIBRS Not affected; BHI Retpoline Vulnerability Srbds: Unknown: Dependent on hypervisor status Vulnerability Tsx async abort: Mitigation; Clear CPU buffers; SMT Host state unknown make[1]: [debian/rules:75: override_dh_auto_test-arch] Error 255 (ignored) export BIN=/build/reproducible-path/vg-1.59.0+ds/debian/help/vg-plain \ ; echo "Testing ${BIN}" \ && cp -v "${BIN}" "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg" \ && . /build/reproducible-path/vg-1.59.0+ds/source_me.sh \ && ( cd /build/reproducible-path/vg-1.59.0+ds/test && prove -v t/ ) Testing /build/reproducible-path/vg-1.59.0+ds/debian/help/vg-plain '/build/reproducible-path/vg-1.59.0+ds/debian/help/vg-plain' -> '/build/reproducible-path/vg-1.59.0+ds/debian/help/vg' t/00_unittest.t: line 12: vg: command not found t/00_unittest.t ....... 1..1 not ok 1 - vg unit tests complete successfully # got: '127' # expected: '0' Failed 1/1 subtests t/01_build_graph.t .... 1..1 ok 1 - graph building with the API ok t/02_vg_construct.t: line 12: vg: command not found t/02_vg_construct.t: line 12: vg: command not found t/02_vg_construct.t: line 14: vg: command not found t/02_vg_construct.t: line 14: vg: command not found t/02_vg_construct.t: line 16: vg: command not found t/02_vg_construct.t: line 16: vg: command not found t/02_vg_construct.t: line 18: vg: command not found t/02_vg_construct.t: line 21: vg: command not found t/02_vg_construct.t: line 24: vg: command not found t/02_vg_construct.t: line 28: vg: command not found t/02_vg_construct.t: line 33: vg: command not found t/02_vg_construct.t: line 33: vg: command not found t/02_vg_construct.t: line 35: vg: command not found t/02_vg_construct.t: line 38: vg: command not found t/02_vg_construct.t: line 41: vg: command not found t/02_vg_construct.t: line 46: vg: command not found t/02_vg_construct.t: line 47: vg: command not found t/02_vg_construct.t: line 51: vg: command not found t/02_vg_construct.t: line 56: vg: command not found t/02_vg_construct.t: line 56: vg: command not found t/02_vg_construct.t: line 56: vg: command not found t/02_vg_construct.t: line 56: vg: command not found t/02_vg_construct.t: line 56: vg: command not found t/02_vg_construct.t: line 56: vg: command not found t/02_vg_construct.t: line 56: vg: command not found t/02_vg_construct.t: line 56: vg: command not found t/02_vg_construct.t: line 56: vg: command not found t/02_vg_construct.t: line 56: vg: command not found t/02_vg_construct.t: line 56: vg: command not found t/02_vg_construct.t: line 56: vg: command not found t/02_vg_construct.t: line 56: vg: command not found 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t/02_vg_construct.t: line 107: vg: command not found t/02_vg_construct.t: line 109: vg: command not found t/02_vg_construct.t: line 109: vg: command not found t/02_vg_construct.t: line 111: vg: command not found t/02_vg_construct.t: line 111: vg: command not found t/02_vg_construct.t: line 111: vg: command not found t/02_vg_construct.t: line 119: vg: command not found t/02_vg_construct.t: line 121: vg: command not found t/02_vg_construct.t ... 1..30 not ok 1 - unnamed test # got: '210' # expected: 'construction produces the right number of nodes' not ok 2 - unnamed test # got: '291' # expected: 'construction produces the right number of edges' not ok 3 - unnamed test # got: '2' # expected: 'construction obeys rename and region options' not ok 4 - construction of a 1 megabase graph from the 1000 Genomes succeeds # got: '127' # expected: '0' not ok 5 - unnamed test # got: '84559' # expected: 'the 1mb graph has the expected number of nodes' not ok 6 - unnamed test # got: '115375' # expected: 'the 1mb graph has the expected number of edges' not ok 7 - vg construct can skip self-inconsistent structural variants # got: '127' # expected: '0' ok 8 - node size is manageable by default not ok 9 - construction of a very complex region succeeds # got: '127' # expected: '0' not ok 10 - unnamed test # got: '71' # expected: 'the complex graph has the expected number of nodes' not ok 11 - unnamed test # got: '116' # expected: 'the complex graph has the expected number of edges' ok 12 - the ordering of variants at the same position has no effect on the resulting graph not ok 13 - construction does not fail when the first position in the VCF is repeated and has an indel # got: '127' # expected: '0' ok 14 - the size of the regions used in construction has no effect on the graph ok 15 - the number of threads used in construction has no effect on the graph ok 16 - the number of threads and regions used in construction has no effect on the graph not ok 17 - construction of a graph with two head nodes succeeds # got: '127' # expected: '0' not ok 18 - unnamed test # got: '1074' # expected: 'the graph contains all the sequence in the reference and VCF' not ok 19 - varying the max node size does not affect graph length # got: '0' # expected: '1' not ok 20 - unnamed test # got: '12' # expected: 'nodes are correctly capped in size' not ok 21 - unnamed test # got: '241' # expected: '-R --region flag is respected' not ok 22 - vg construct does not require a vcf # got: '127' # expected: '0' ok 23 - vg construct respects node size limit not ok 24 - --region can be interpreted to be a reference sequence (and not parsed as a region spec) # got: '0' # expected: '1' not ok 25 - vg constructs the correct graph for inversions # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '9f7d23d3c5382229c6c3bf64d1ba44bc' not ok 26 - vg construct skips variants with . ALTs # got: '' # expected: '1' not ok 27 - VCF with * alleles is accepted # got: '127' # expected: '0' not ok 28 - VCF record with * allele is rejected # got: '1' # expected: '0' not ok 29 - Reference with ambiguity codes has them coerced to Ns # got: '127' # expected: '0' not ok 30 - Expected number of Ns are created # got: '0' # expected: '10' Failed 24/30 subtests t/03_vg_view.t: line 10: vg: command not found t/03_vg_view.t: line 10: vg: command not found t/03_vg_view.t: line 11: vg: command not found t/03_vg_view.t: line 11: vg: command not found t/03_vg_view.t: line 13: vg: command not found t/03_vg_view.t: line 13: vg: command not found t/03_vg_view.t: line 13: vg: command not found t/03_vg_view.t: line 13: vg: command not found t/03_vg_view.t: line 15: vg: command not found t/03_vg_view.t: line 15: vg: command not found t/03_vg_view.t: line 17: vg: command not found t/03_vg_view.t: line 17: vg: command not found t/03_vg_view.t: line 17: vg: command not found t/03_vg_view.t: line 17: vg: command not found t/03_vg_view.t: line 17: vg: command not found t/03_vg_view.t: line 17: vg: command not found t/03_vg_view.t: line 20: vg: command not found t/03_vg_view.t: line 20: vg: command not found t/03_vg_view.t: line 20: vg: command not found t/03_vg_view.t: line 20: vg: command not found t/03_vg_view.t: line 24: vg: command not found t/03_vg_view.t: line 24: vg: command not found t/03_vg_view.t: line 24: vg: command not found t/03_vg_view.t: line 25: vg: command not found t/03_vg_view.t: line 25: vg: command not found t/03_vg_view.t: line 28: vg: command not found t/03_vg_view.t: line 31: vg: command not found t/03_vg_view.t: line 32: vg: command not found t/03_vg_view.t: line 32: vg: command not found t/03_vg_view.t: line 37: vg: command not found t/03_vg_view.t: line 37: vg: command not found t/03_vg_view.t: line 39: vg: command not found t/03_vg_view.t: line 39: vg: command not found t/03_vg_view.t: line 41: vg: command not found t/03_vg_view.t: line 41: vg: command not found t/03_vg_view.t: line 43: vg: command not found t/03_vg_view.t: line 45: vg: command not found t/03_vg_view.t: line 48: vg: command not found t/03_vg_view.t: line 48: vg: command not found t/03_vg_view.t: line 49: vg: command not found t/03_vg_view.t: line 65: vg: command not found t/03_vg_view.t: line 66: vg: command not found t/03_vg_view.t: line 66: vg: command not found t/03_vg_view.t: line 70: vg: command not found t/03_vg_view.t: line 71: vg: command not found t/03_vg_view.t: line 71: vg: command not found t/03_vg_view.t: line 77: vg: command not found t/03_vg_view.t ........ 1..23 not ok 1 - view produces the expected number of lines of dot output # got: '0' # expected: '505' not ok 2 - view produces the expected number of lines of GFA output # got: '0' # expected: '503' not ok 3 - view converts back and forth between GFA and vg format # got: '0' # expected: '10' not ok 4 - view can convert BAM to GAM # got: '0' # expected: '3333' ok 5 - view can round-trip JSON and GAM not ok 6 - view can round-trip qualities and encodes tham as PHRED+0 base-64-encoded strings in JSON # got: 'FFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIBBII''''IIIIII'F'IIIIIIII'FIIIIIIIIFFIIIFIIIIIIIFIIIIIIIIIIFIIFIIIIIIIIIIIIIIIIIIIIFIIFIIIFIIIFIIIIIFIIIIIII' # expected: '' ok 7 - view can reconstruct a VG graph from JSON ok 8 - view can pass through VG when loading as vg::VG ok 9 - view can pass through semantically identical VG normally ok 10 - view parses sample names not ok 11 - view can handle fastq input # got: '0' # expected: '2000' not ok 12 - unnamed test # got: '4' # expected: 'view can translate graphs with 2-node cycles' not ok 13 - view outputs properly oriented GFA # got: '0' # expected: '1' not ok 14 - view produces the expected number of lines of dot output from a cyclic graph # got: '0' # expected: '23' not ok 15 - streaming JSON output produces the expected number of chunks # got: '0' # expected: '4' not ok 16 - duplicate warnings can be suppressed when loading as vg::VG # got: '1' # expected: '0' not ok 17 - gfa graphs with overlaps are rejected # got: '127' # expected: '1' not ok 18 - GFA import produces a concise error message when overlaps are present # got: '1' # expected: '2' not ok 19 - GFA import rejects a GFA file with an overlap that goes beyond its sequences # got: '127' # expected: '1' not ok 20 - GFA import produces a concise error message in that case # got: '1' # expected: '2' ok 21 - vg view preserves path metadata of rGFA file ok 22 - vg view preserves path metadata of GFA file not ok 23 - vg view can emit a GFA file with subranges on a haplotype without explicit phase blocks # got: '127' # expected: '0' Failed 16/23 subtests t/04_vg_align.t: line 10: vg: command not found t/04_vg_align.t: line 12: vg: command not found t/04_vg_align.t: line 14: vg: command not found t/04_vg_align.t: line 16: vg: command not found t/04_vg_align.t: line 18: vg: command not found t/04_vg_align.t: line 20: vg: command not found t/04_vg_align.t: line 22: vg: command not found t/04_vg_align.t: line 26: vg: command not found t/04_vg_align.t: line 28: vg: command not found t/04_vg_align.t: line 30: vg: command not found t/04_vg_align.t: line 32: vg: command not found t/04_vg_align.t: line 34: vg: command not found t/04_vg_align.t: line 36: vg: command not found t/04_vg_align.t: line 38: vg: command not found t/04_vg_align.t: line 40: vg: command not found t/04_vg_align.t: line 40: vg: command not found t/04_vg_align.t: line 41: vg: command not found t/04_vg_align.t: line 41: vg: command not found t/04_vg_align.t: line 41: vg: command not found t/04_vg_align.t: line 45: vg: command not found t/04_vg_align.t: line 47: vg: command not found t/04_vg_align.t: line 50: vg: command not found t/04_vg_align.t: line 53: vg: command not found t/04_vg_align.t: line 56: vg: command not found t/04_vg_align.t: line 59: vg: command not found t/04_vg_align.t: line 61: vg: command not found t/04_vg_align.t ....... 1..20 not ok 1 - alignment traverses the correct path # got: '0' # expected: '4' not ok 2 - unnamed test # got: '48' # expected: 'alignment score is as expected' not ok 3 - unnamed test # got: '58' # expected: 'full length bonus works and is included by default' not ok 4 - unnamed test # got: '37' # expected: 'bonuses are included on only one end for pinned alignments' not ok 5 - unnamed test # got: '96' # expected: 'scoring parameters are respected' not ok 6 - unnamed test # got: '96' # expected: 'score-matrix file should give same results as --match 2 --mismatch 2: scoring parameters are respected' not ok 7 - unnamed test # got: '70211814' # expected: 'alignment does not contain excessive soft clips under lenient scoring' not ok 8 - unnamed test # got: '70211814' # expected: 'score-matrix file should give same results as --match 2 --mismatch 2: alignment does not contain excessive soft clips under lenient scoring' not ok 9 - unnamed test # got: '274' # expected: 'alignment score does not overflow at 255 when using 8x16bit vectors' not ok 10 - unnamed test # got: '274' # expected: 'score-matrix file should give same results as --match 2 --mismatch 2: alignment score does not overflow at 255 when using 8x16bit vectors' not ok 11 - unnamed test # got: '280136076' # expected: 'Ns do not cause excessive soft clipping' not ok 12 - unnamed test # got: '59867694' # expected: 'nodes are only referenced if they have mappings' not ok 13 - align can use query names and outputs GAM # got: '0' # expected: '4' not ok 14 - alignment to cyclic graphs works # got: '0' # expected: '1' not ok 15 - graphs where duplicated nodes need flipping can be used for alignment # got: '127' # expected: '0' not ok 16 - node flipping doesn't destroy the alignment # got: '127' # expected: '0' not ok 17 - alignment correctly handles an inversion # got: '127' # expected: '0' not ok 18 - the exploding graph doesn't blow up # got: '127' # expected: '0' not ok 19 - unnamed test # got: '1' # expected: 'pinning doesn't cause problems for gssw' not ok 20 - unnamed test # got: '1' # expected: 'left pinning is correctly handled' Failed 20/20 subtests t/05_vg_find.t: line 10: vg: command not found t/05_vg_find.t: line 14: vg: command not found t/05_vg_find.t: line 14: vg: command not found t/05_vg_find.t: line 16: vg: command not found t/05_vg_find.t: line 16: vg: command not found t/05_vg_find.t: line 18: vg: command not found t/05_vg_find.t: line 19: vg: command not found t/05_vg_find.t: line 21: vg: command not found t/05_vg_find.t: line 22: vg: command not found t/05_vg_find.t: line 23: vg: command not found t/05_vg_find.t: line 24: vg: command not found t/05_vg_find.t: line 25: vg: command not found t/05_vg_find.t: line 27: vg: command not found t/05_vg_find.t: line 27: vg: command not found t/05_vg_find.t: line 29: vg: command not found t/05_vg_find.t: line 29: vg: command not found t/05_vg_find.t: line 33: vg: command not found t/05_vg_find.t: line 34: vg: command not found t/05_vg_find.t: line 34: vg: command not found t/05_vg_find.t: line 35: vg: command not found t/05_vg_find.t: line 35: vg: command not found rm: cannot remove 'm.xg': No such file or directory t/05_vg_find.t: line 38: vg: command not found t/05_vg_find.t: line 39: vg: command not found t/05_vg_find.t: line 40: vg: command not found t/05_vg_find.t: line 43: vg: command not found t/05_vg_find.t: line 44: vg: command not found t/05_vg_find.t: line 45: vg: command not found t/05_vg_find.t: line 46: vg: command not found t/05_vg_find.t: line 46: vg: command not found t/05_vg_find.t: line 61: vg: command not found t/05_vg_find.t: line 62: vg: command not found t/05_vg_find.t: line 63: vg: command not found t/05_vg_find.t: line 65: vg: command not found t/05_vg_find.t: line 66: vg: command not found t/05_vg_find.t: line 66: vg: command not found t/05_vg_find.t: line 67: vg: command not found t/05_vg_find.t: line 67: vg: command not found t/05_vg_find.t: line 67: vg: command not found t/05_vg_find.t: line 71: vg: command not found t/05_vg_find.t: line 71: vg: command not found t/05_vg_find.t: line 75: vg: command not found t/05_vg_find.t: line 76: vg: command not found t/05_vg_find.t: line 77: vg: command not found t/05_vg_find.t: line 77: vg: command not found t/05_vg_find.t: line 81: vg: command not found t/05_vg_find.t: line 81: vg: command not found t/05_vg_find.t: line 84: vg: command not found t/05_vg_find.t: line 85: vg: command not found t/05_vg_find.t: line 86: vg: command not found t/05_vg_find.t: line 86: vg: command not found t/05_vg_find.t: line 90: vg: command not found t/05_vg_find.t: line 90: vg: command not found t/05_vg_find.t: line 91: vg: command not found t/05_vg_find.t: line 92: vg: command not found t/05_vg_find.t: line 93: vg: command not found t/05_vg_find.t: line 94: vg: command not found t/05_vg_find.t: line 94: vg: command not found t/05_vg_find.t: line 94: vg: command not found t/05_vg_find.t: line 97: vg: command not found t/05_vg_find.t: line 98: vg: command not found t/05_vg_find.t: line 99: vg: command not found t/05_vg_find.t: line 99: vg: command not found t/05_vg_find.t: line 101: vg: command not found t/05_vg_find.t: line 102: vg: command not found t/05_vg_find.t: line 102: vg: command not found t/05_vg_find.t: line 106: vg: command not found t/05_vg_find.t: line 107: vg: command not found t/05_vg_find.t: line 107: vg: command not found t/05_vg_find.t: line 107: vg: command not found t/05_vg_find.t: line 107: vg: command not found t/05_vg_find.t: line 109: vg: command not found t/05_vg_find.t: line 114: vg: command not found t/05_vg_find.t: line 115: vg: command not found t/05_vg_find.t: line 116: vg: command not found t/05_vg_find.t: line 119: vg: command not found t/05_vg_find.t: line 119: vg: command not found t/05_vg_find.t: line 119: vg: command not found t/05_vg_find.t: line 119: vg: command not found t/05_vg_find.t: line 120: vg: command not found t/05_vg_find.t: line 120: vg: command not found t/05_vg_find.t: line 127: vg: command not found t/05_vg_find.t: line 128: vg: command not found t/05_vg_find.t: line 137: vg: command not found cmp: EOF on found.gfa which is empty t/05_vg_find.t ........ 1..29 not ok 1 - construction # got: '127' # expected: '0' not ok 2 - unnamed test # got: '72' # expected: 'a path can be queried from the xg index' not ok 3 - a node near another can be obtained using context from the xg index # got: '0' # expected: '1' not ok 4 - each perfect read contains one maximal exact match # got: '0' # expected: '100' not ok 5 - unnamed test # got: '8' # expected: 'vg find -D finds approximate distance between 2 adjacent node starts' not ok 6 - unnamed test # got: '8' # expected: 'vg find -D finds approximate distance between node start and adjacent snp' not ok 7 - unnamed test # got: '7' # expected: 'vg find -D jumps deletion' not ok 8 - unnamed test # got: '7' # expected: 'vg find -D jumps deletion from other allele in snp' not ok 9 - vg find -L finds same number of nodes (with -c 1) # got: '0' # expected: '5' not ok 10 - vg find -L works with -r. it scans from start position of first node in range # got: '0' # expected: '3' not ok 11 - vg find -L tracks length from start position of input node # got: '0' # expected: '5' not ok 12 - vg find -L works with more than one input node # got: '0' # expected: '7' not ok 13 - unnamed test # got: '[["ACC",["1:-32"]],["CCGTTAG",["1:5"]],["GTTAGAGT",["1:19"]],["TAGAGTCAG",["1:40"]]]' # expected: 'we find the 4 canonical SMEMs from @lh3's bwa mem poster' not ok 14 - we can find the right MEMs for a sequence with Ns # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: 'f33b1420b5dc5126f5e74eecc6b79503' ok 15 - we find the same MEMs sequences with different lengths of Ns not ok 16 - the GAM index can return the set of alignments mapping to a node # got: '0' # expected: '6' not ok 17 - a subgraph query may be used to obtain a particular subset of alignments from a sorted GAM # got: '0' # expected: '15' not ok 18 - the index can be queried using GAM alignments # got: '0' # expected: '1' not ok 19 - find gets connected edges between queried nodes by default # got: '0' # expected: '4' not ok 20 - find gets nodes provided in a node file list # got: '0' # expected: '4' not ok 21 - extracting by path adds no extra edges # got: '' # expected: '1' ok 22 - pattern based path extraction works not ok 23 - path DAG range query works # got: '0' # expected: '4' not ok 24 - we can extract a set of targets to separate files # got: '0' # expected: '20' ok 25 - the same extraction can be made using BED input not ok 26 - we see the expected number of kmers in the given targets # got: '0' # expected: '36' not ok 27 - unnamed test # got: '1510' # expected: 'we find the expected number of kmers with haplotype frequency equal to 2' ok 28 - GFA i/o for find -n consistent with converting both ways not ok 29 - find nodes that map to the provided node ids # got: '1' # expected: '0' Failed 25/29 subtests t/06_vg_index.t: line 13: vg: command not found t/06_vg_index.t: line 15: vg: command not found t/06_vg_index.t: line 18: vg: command not found t/06_vg_index.t: line 21: vg: command not found cmp: x.xg: No such file or directory t/06_vg_index.t: line 27: vg: command not found cmp: x.gcsa: No such file or directory t/06_vg_index.t: line 40: vg: command not found t/06_vg_index.t: line 42: vg: command not found t/06_vg_index.t: line 45: vg: command not found t/06_vg_index.t: line 48: vg: command not found t/06_vg_index.t: line 50: vg: command not found t/06_vg_index.t: line 53: vg: command not found t/06_vg_index.t: line 53: vg: command not found t/06_vg_index.t: line 55: vg: command not found t/06_vg_index.t: line 58: vg: command not found cmp: x.xg: No such file or directory t/06_vg_index.t: line 64: vg: command not found cmp: x.gbwt: No such file or directory t/06_vg_index.t: line 70: vg: command not found t/06_vg_index.t: line 70: vg: command not found t/06_vg_index.t: line 73: vg: command not found t/06_vg_index.t: line 75: vg: command not found t/06_vg_index.t: line 78: vg: command not found t/06_vg_index.t: line 79: vg: command not found t/06_vg_index.t: line 81: vg: command not found t/06_vg_index.t: line 82: vg: command not found cmp: x-gaf.gbwt: No such file or directory t/06_vg_index.t: line 95: vg: command not found t/06_vg_index.t: line 108: vg: command not found t/06_vg_index.t: line 110: vg: command not found t/06_vg_index.t: line 113: vg: command not found t/06_vg_index.t: line 116: vg: command not found cmp: xy.xg: No such file or directory t/06_vg_index.t: line 130: vg: command not found t/06_vg_index.t: line 132: vg: command not found t/06_vg_index.t: line 135: vg: command not found t/06_vg_index.t: line 138: vg: command not found t/06_vg_index.t: line 141: vg: command not found t/06_vg_index.t: line 144: vg: command not found t/06_vg_index.t: line 147: vg: command not found cmp: xy.xg: No such file or directory t/06_vg_index.t: line 163: vg: command not found t/06_vg_index.t: line 173: vg: command not found t/06_vg_index.t: line 177: vg: command not found t/06_vg_index.t: line 178: vg: command not found t/06_vg_index.t: line 182: vg: command not found t/06_vg_index.t: line 183: vg: command not found t/06_vg_index.t: line 183: vg: command not found t/06_vg_index.t: line 186: vg: command not found t/06_vg_index.t: line 187: vg: command not found t/06_vg_index.t: line 189: x1337.sorted.gam.gai: No such file or directory t/06_vg_index.t: line 189: x1337.sorted.gam.gai2: No such file or directory t/06_vg_index.t: line 194: vg: command not found t/06_vg_index.t: line 195: vg: command not found t/06_vg_index.t: line 196: vg: command not found t/06_vg_index.t: line 198: vg: command not found t/06_vg_index.t: line 200: vg: command not found t/06_vg_index.t: line 208: vg: command not found t/06_vg_index.t: line 211: vg: command not found t/06_vg_index.t: line 217: vg: command not found t/06_vg_index.t: line 227: vg: command not found t/06_vg_index.t: line 229: vg: command not found t/06_vg_index.t: line 233: vg: command not found t/06_vg_index.t: line 246: vg: command not found t/06_vg_index.t: line 248: vg: command not found t/06_vg_index.t: line 251: vg: command not found t/06_vg_index.t: line 254: vg: command not found t/06_vg_index.t: line 254: vg: command not found t/06_vg_index.t: line 257: vg: command not found t/06_vg_index.t: line 257: vg: command not found t/06_vg_index.t: line 263: vg: command not found t/06_vg_index.t: line 264: vg: command not found t/06_vg_index.t: line 265: vg: command not found t/06_vg_index.t: line 268: vg: command not found cat: graph.gbz: No such file or directory t/06_vg_index.t ....... 1..54 not ok 1 - building an XG index of a graph # got: '127' # expected: '0' not ok 2 - building a GCSA index of a graph # got: '127' # expected: '0' not ok 3 - building both indexes at once # got: '127' # expected: '0' not ok 4 - the indexes are identical when built one at a time and together # got: '2' # expected: '0' not ok 5 - building GCSA from XG # got: '127' # expected: '0' not ok 6 - the GCSA indexes are identical when built from vg and from xg # got: '2' # expected: '0' not ok 7 - building a GBWT index of a graph with haplotypes # got: '127' # expected: '0' not ok 8 - building an XG index of a graph with haplotypes # got: '127' # expected: '0' not ok 9 - xg index does not contain alt paths by default # got: '0' # expected: '1' not ok 10 - building an XG index of a graph with haplotypes and alt paths included # got: '127' # expected: '0' ok 11 - xg index does contains alt paths with index -L not ok 12 - building a GCSA index of a graph with haplotypes # got: '127' # expected: '0' not ok 13 - building all indexes at once # got: '127' # expected: '0' not ok 14 - the indexes are identical # got: '2' # expected: '0' not ok 15 - building all indexes at once, while leaving alt paths in xg # got: '127' # expected: '0' not ok 16 - the indexes are identical with -L # got: '2' # expected: '0' ok 17 - xg index does contains alt paths with index -L all at once not ok 18 - samples can be excluded from haplotype indexing # got: '127' # expected: '0' not ok 19 - unnamed test # got: '0' # expected: 'excluded samples were not included in the GBWT index' not ok 20 - GBWT from GAF same as from GAM # got: '2' # expected: '0' not ok 21 - building GBWT index for a regional graph # got: '127' # expected: '0' not ok 22 - no warnings about missing variants produced # got: '48' # expected: '0' not ok 23 - building an XG index of multiple graphs # got: '127' # expected: '0' not ok 24 - building a GCSA index of multiple graphs # got: '127' # expected: '0' not ok 25 - building both indexes at once # got: '127' # expected: '0' not ok 26 - the indexes are identical # got: '2' # expected: '0' not ok 27 - building a GBWT index of multiple graphs with haplotypes # got: '127' # expected: '0' not ok 28 - building an XG index of multiple graphs with haplotypes # got: '127' # expected: '0' not ok 29 - building a GCSA index of multiple graphs with haplotypes # got: '127' # expected: '0' not ok 30 - building XG and GCSA indexes at once # got: '127' # expected: '0' not ok 31 - building an XG index with alt paths # got: '127' # expected: '0' not ok 32 - building a GBWT index from an XG index # got: '127' # expected: '0' not ok 33 - the indexes are identical # got: '2' # expected: '0' not ok 34 - GBWT can be built for paths # got: '127' # expected: '0' not ok 35 - fail with nonexistent file # got: '127' # expected: '1' not ok 36 - a prebuilt deBruijn graph in GCSA2 format may be used # got: '127' # expected: '0' ok 37 - vg index and vg gamsort produce identical sorted GAM indexes not ok 38 - storage of multiple graphs in an index succeeds # got: '127' # expected: '0' not ok 39 - can index backward nodes # got: '127' # expected: '0' not ok 40 - can index kmers for backward nodes # got: '127' # expected: '0' not ok 41 - GCSA2 index works on cyclic graphs with heads and tails # got: '0' # expected: '1' not ok 42 - GCSA2 index works on cyclic graphs with no heads or tails # got: '0' # expected: '1' not ok 43 - GCSA2 index works on cyclic graphs with self loops # got: '0' # expected: '1' not ok 44 - GCSA2 index works on general cyclic graphs # got: '0' # expected: '1' not ok 45 - GCSA2 indexing of a tiny graph works # got: '0' # expected: '1' not ok 46 - GCSA2 indexing succeeds on a single-node graph # got: '0' # expected: '1' not ok 47 - GCSA2 indexing succeeds on graph with heads but no tails # got: '0' # expected: '1' not ok 48 - a useful error message is produced when nodes are too large # got: '0' # expected: '1' not ok 49 - snarl finding with trivial snarls # got: '127' # expected: '0' not ok 50 - building a distance index of a graph # got: '127' # expected: '0' not ok 51 - building a distance index of a piped vg graph # got: '127' # expected: '0' not ok 52 - building a distance index of a piped PackedGraph # got: '127' # expected: '0' not ok 53 - distance index construction from GBZ # got: '127' # expected: '0' not ok 54 - distance index construction from piped GBZ # got: '127' # expected: '0' Failed 51/54 subtests t/07_vg_map.t: line 10: vg: command not found t/07_vg_map.t: line 11: vg: command not found t/07_vg_map.t: line 13: vg: command not found t/07_vg_map.t: line 15: vg: command not found t/07_vg_map.t: line 17: vg: command not found t/07_vg_map.t: line 19: vg: command not found t/07_vg_map.t: line 21: vg: command not found t/07_vg_map.t: line 23: vg: command not found t/07_vg_map.t: line 25: vg: command not found t/07_vg_map.t: line 27: vg: command not found t/07_vg_map.t: line 29: vg: command not found t/07_vg_map.t: line 31: vg: command not found t/07_vg_map.t: line 33: vg: command not found t/07_vg_map.t: line 35: vg: command not found t/07_vg_map.t: line 38: vg: command not found t/07_vg_map.t: line 40: vg: command not found t/07_vg_map.t: line 40: vg: command not found t/07_vg_map.t: line 40: vg: command not found t/07_vg_map.t: line 43: vg: command not found t/07_vg_map.t: line 43: vg: command not found t/07_vg_map.t: line 43: vg: command not found t/07_vg_map.t: line 47: vg: command not found t/07_vg_map.t: line 49: vg: command not found t/07_vg_map.t: line 51: vg: command not found printf: usage: printf [-v var] format [arguments] t/07_vg_map.t: line 54: vg: command not found t/07_vg_map.t: line 56: vg: command not found t/07_vg_map.t: line 62: vg: command not found t/07_vg_map.t: line 63: vg: command not found t/07_vg_map.t: line 65: vg: command not found t/07_vg_map.t: line 65: vg: command not found t/07_vg_map.t: line 67: vg: command not found t/07_vg_map.t: line 67: vg: command not found t/07_vg_map.t: line 69: vg: command not found t/07_vg_map.t: line 69: vg: command not found t/07_vg_map.t: line 71: vg: command not found t/07_vg_map.t: line 71: vg: command not found t/07_vg_map.t: line 72: vg: command not found t/07_vg_map.t: line 72: vg: command not found t/07_vg_map.t: line 94: vg: command not found t/07_vg_map.t: line 95: vg: command not found t/07_vg_map.t: line 96: vg: command not found t/07_vg_map.t: line 101: vg: command not found t/07_vg_map.t: line 102: vg: command not found t/07_vg_map.t: line 106: vg: command not found t/07_vg_map.t: line 107: vg: command not found t/07_vg_map.t: line 108: vg: command not found t/07_vg_map.t: line 110: vg: command not found t/07_vg_map.t: line 112: vg: command not found t/07_vg_map.t: line 114: vg: command not found t/07_vg_map.t: line 115: vg: command not found t/07_vg_map.t: line 123: vg: command not found t/07_vg_map.t: line 124: vg: command not found t/07_vg_map.t: line 128: vg: command not found t/07_vg_map.t: line 129: vg: command not found t/07_vg_map.t: line 135: vg: command not found t/07_vg_map.t: line 136: vg: command not found t/07_vg_map.t: line 141: vg: command not found t/07_vg_map.t: line 144: vg: command not found t/07_vg_map.t: line 147: vg: command not found t/07_vg_map.t: line 150: vg: command not found t/07_vg_map.t: line 154: vg: command not found t/07_vg_map.t: line 155: vg: command not found t/07_vg_map.t: line 158: vg: command not found t/07_vg_map.t: line 160: vg: command not found t/07_vg_map.t: line 161: vg: command not found t/07_vg_map.t: line 163: vg: command not found t/07_vg_map.t: line 166: vg: command not found t/07_vg_map.t: line 166: vg: command not found t/07_vg_map.t: line 166: vg: command not found t/07_vg_map.t: line 174: vg: command not found t/07_vg_map.t: line 174: vg: command not found t/07_vg_map.t: line 174: vg: command not found t/07_vg_map.t: line 183: vg: command not found t/07_vg_map.t: line 184: vg: command not found t/07_vg_map.t: line 185: vg: command not found t/07_vg_map.t: line 191: vg: command not found t/07_vg_map.t: line 195: vg: command not found t/07_vg_map.t: line 196: vg: command not found t/07_vg_map.t: line 197: vg: command not found t/07_vg_map.t ......... 1..55 not ok 1 - offset counts unused bases from the start of the node on the forward strand # got: '' # expected: '3' not ok 2 - xdrop alignment obtains the expected result # got: '' # expected: '3' not ok 3 - xdrop alignment obtains the expected result for the reverse complement # got: '' # expected: '5' not 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 # got: '' # expected: '3' not ok 5 - offset counts unused bases from the start of the node on the reverse strand # got: '' # expected: '5' not ok 6 - global alignment traverses the correct path # got: '0' # expected: '4' not ok 7 - alignment score is as expected # got: '' # expected: '58' not ok 8 - scoring parameters are respected # got: '' # expected: '106' not ok 9 - score-matrix file should give same results as --match 2 --mismatch 2: scoring parameters are respected # got: '' # expected: '106' not ok 10 - full length bonus always be included # got: '' # expected: '58' not ok 11 - full length bonus can be set to 0 # got: '' # expected: '96' not ok 12 - vg map takes -d as input without a variant graph # got: '127' # expected: '0' not ok 13 - vg map can align across a SNP # got: '0' # expected: '1' not ok 14 - alignment works on a small graph # got: '0' # expected: '1000' ok 15 - binary alignment format is equivalent to json version ok 16 - alignment from BAM correctly handles qualities not ok 17 - chunky-banded alignment works # got: '0' # expected: '1' not ok 18 - unnamed test # got: '' # expected: 'multiple alignments are returned in descending score order' not ok 19 - only a single primary alignment is returned # got: '0' # expected: '1' not ok 20 - vg can map multi-line FASTA sequences # got: '127' # expected: '0' not ok 21 - mapping of BAM file produces expected number of alignments # got: '0' # expected: '3333' not ok 22 - mapping from a fastq produces the expected number of alignments # got: '0' # expected: '3327' ok 23 - allowing secondary alignments with MEM mapping does not change number of primary alignments ok 24 - vg connects paired-end reads in gam output not ok 25 - mapping to graphs that can't be oriented without swapping edges works correctly # got: '127' # expected: '0' not ok 26 - reads multi-map to multiple possible locations # got: '0' # expected: '1' not ok 27 - vg map works based on gcsa and xg indexes # got: '0' # expected: '1000' not ok 28 - unnamed test # got: '30' # expected: 'the mapping quality may be capped' not ok 29 - paired read alignments forced to be consistent have lower score than unrestricted alignments # got: '0' # expected: '1' not ok 30 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments # got: '0' # expected: '1' not ok 31 - only primary alignments have mapping quality scores # got: '0' # expected: '2' not ok 32 - unpaired reads produce mapping quality scores # got: '0' # expected: '1000' ok 33 - map returns same output on xg and vg (single threaded) not ok 34 - unnamed test # got: '10' # expected: 'base quality adjusted alignment produces higher scores if mismatches have low quality' not ok 35 - error on vg map -f (unpaired) # got: '127' # expected: '1' not ok 36 - error on vg map -f (interleaved) # got: '127' # expected: '1' not ok 37 - error on vg map -f (paired, LHS) # got: '127' # expected: '1' not ok 38 - error on vg map -f (paired, RHS) # got: '127' # expected: '1' not ok 39 - mapping a read that touches unused nodes gets the base score # got: '' # expected: '36' not ok 40 - mapping a read that matches a haplotype gets a small penalty # got: '' # expected: '35' not ok 41 - mapping a read that matches a haplotype with exponent 0 gets the base score # got: '' # expected: '36' not ok 42 - mapping a read that matches no haplotypes gets a larger penalty # got: '' # expected: '21' not ok 43 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 44 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 45 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 46 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 47 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '163 # 83' not ok 48 - surjection of unpaired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 49 - surjection of unpaired reads to SAM yields correct pair partner positions # got: '' # expected: '0 # 0' not ok 50 - surjection of unpaired reads to SAM yields distinct QNAMEs # got: '0' # expected: '2' not ok 51 - surjection of unpaired reads to SAM produces absent partner contigs # got: '' # expected: '* # *' not ok 52 - surjection of unpaired reads to SAM produces correct flags # got: '' # expected: '0 # 16' not ok 53 - unnamed test # got: '1' # expected: 'mapper can read FASTA input' not ok 54 - unnamed test # got: '1' # expected: 'mapper can read multiline FASTA input' not ok 55 - unnamed test # got: '130' # expected: 'xdrop works on a reversed read' Failed 50/55 subtests t/08_vg_ids.t: line 10: vg: command not found t/08_vg_ids.t: line 10: vg: command not found t/08_vg_ids.t: line 10: vg: command not found t/08_vg_ids.t: line 12: vg: command not found t/08_vg_ids.t: line 12: vg: command not found t/08_vg_ids.t: line 12: vg: command not found t/08_vg_ids.t: line 12: vg: command not found t/08_vg_ids.t: line 14: vg: command not found t/08_vg_ids.t: line 14: vg: command not found t/08_vg_ids.t: line 14: vg: command not found t/08_vg_ids.t: line 14: vg: command not found t/08_vg_ids.t: line 16: vg: command not found t/08_vg_ids.t: line 17: vg: command not found t/08_vg_ids.t: line 18: vg: command not found t/08_vg_ids.t: line 20: vg: command not found t/08_vg_ids.t: line 22: vg: command not found t/08_vg_ids.t: line 23: vg: command not found (standard_in) 1: syntax error t/08_vg_ids.t: line 29: vg: command not found t/08_vg_ids.t: line 32: vg: command not found t/08_vg_ids.t: line 35: vg: command not found t/08_vg_ids.t: line 35: vg: command not found t/08_vg_ids.t: line 39: vg: command not found t/08_vg_ids.t: line 39: vg: command not found t/08_vg_ids.t: line 41: vg: command not found t/08_vg_ids.t: line 41: vg: command not found t/08_vg_ids.t: line 41: vg: command not found t/08_vg_ids.t: line 42: vg: command not found t/08_vg_ids.t: line 42: vg: command not found t/08_vg_ids.t: line 42: vg: command not found t/08_vg_ids.t: line 42: vg: command not found t/08_vg_ids.t: line 43: vg: command not found t/08_vg_ids.t: line 43: vg: command not found t/08_vg_ids.t: line 43: vg: command not found t/08_vg_ids.t: line 43: vg: command not found t/08_vg_ids.t ......... 1..10 not ok 1 - unnamed test # got: '1' # expected: 'minimum node as expected (id compaction correct)' not ok 2 - unnamed test # got: '0' # expected: 'maximum node is as expected (id compaction correct)' not ok 3 - unnamed test # got: 'correctly generated joint id space for several graphs' # expected: '' not ok 4 - can sort and re-number a graph with self loops # got: '127' # expected: '0' not ok 5 - can sort and renumber a complex cyclic graph # got: '127' # expected: '0' ok 6 - sorting removes back-edges in a DAG not ok 7 - unnamed test # got: 'true' # expected: 'sorting assigns node IDs in topological order' not ok 8 - unnamed test # got: 'sorting does not affect id range' # expected: '' not ok 9 - unnamed test # got: 'sorting does not affect id range of vg' # expected: '' not ok 10 - unnamed test # got: 'sorting does not affect id range of hg' # expected: '' Failed 9/10 subtests t/09_vg_concat.t: line 10: vg: command not found t/09_vg_concat.t: line 12: vg: command not found t/09_vg_concat.t: line 13: vg: command not found t/09_vg_concat.t: line 17: vg: command not found t/09_vg_concat.t: line 17: vg: command not found t/09_vg_concat.t: line 18: vg: command not found t/09_vg_concat.t: line 18: vg: command not found t/09_vg_concat.t: line 22: vg: command not found t/09_vg_concat.t: line 24: vg: command not found t/09_vg_concat.t: line 25: vg: command not found t/09_vg_concat.t: line 27: vg: command not found t/09_vg_concat.t: line 27: vg: command not found t/09_vg_concat.t: line 29: vg: command not found t/09_vg_concat.t: line 29: vg: command not found t/09_vg_concat.t ...... 1..4 ok 1 - concat doubles the number of nodes not ok 2 - concat doubles the number of edges + 1 # got: '0' # expected: '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 2/4 subtests t/100_code_quality.t .. 1..1 ok 1 - code quality is acceptable ok t/10_vg_stats.t: line 10: vg: command not found t/10_vg_stats.t: line 13: vg: command not found t/10_vg_stats.t: line 14: vg: command not found t/10_vg_stats.t: line 17: vg: command not found t/10_vg_stats.t: line 18: vg: command not found t/10_vg_stats.t: line 21: vg: command not found t/10_vg_stats.t: line 22: vg: command not found t/10_vg_stats.t: line 25: vg: command not found t/10_vg_stats.t: line 28: vg: command not found t/10_vg_stats.t: line 33: vg: command not found t/10_vg_stats.t: line 34: vg: command not found t/10_vg_stats.t: line 35: vg: command not found t/10_vg_stats.t: line 38: vg: command not found t/10_vg_stats.t: line 39: vg: command not found t/10_vg_stats.t: line 40: vg: command not found t/10_vg_stats.t: line 41: vg: command not found t/10_vg_stats.t: line 43: vg: command not found t/10_vg_stats.t: line 43: vg: command not found t/10_vg_stats.t: line 45: vg: command not found t/10_vg_stats.t: line 48: vg: command not found t/10_vg_stats.t: line 48: vg: command not found t/10_vg_stats.t: line 51: vg: command not found t/10_vg_stats.t: line 52: vg: command not found t/10_vg_stats.t: line 55: vg: command not found t/10_vg_stats.t: line 56: vg: command not found t/10_vg_stats.t: line 57: vg: command not found t/10_vg_stats.t: line 58: vg: command not found t/10_vg_stats.t: line 59: vg: command not found t/10_vg_stats.t: line 60: vg: command not found t/10_vg_stats.t: line 61: vg: command not found t/10_vg_stats.t: line 62: vg: command not found t/10_vg_stats.t: line 63: vg: command not found t/10_vg_stats.t: line 64: vg: command not found t/10_vg_stats.t: line 65: vg: command not found t/10_vg_stats.t: line 67: vg: command not found t/10_vg_stats.t: line 68: vg: command not found t/10_vg_stats.t: line 71: vg: command not found t/10_vg_stats.t: line 71: vg: command not found t/10_vg_stats.t: line 79: vg: command not found t/10_vg_stats.t: line 82: vg: command not found cmp: EOF on loops.txt which is empty t/10_vg_stats.t: line 89: vg: command not found cmp: EOF on nondeterministic.txt which is empty t/10_vg_stats.t ....... 1..21 not ok 1 - unnamed test # got: '0' # expected: 'vg stats reports the expected number of nodes' not ok 2 - unnamed test # got: '0' # expected: 'vg stats reports the expected number of edges' not ok 3 - unnamed test # got: '0' # expected: 'vg stats reports the expected graph length' not ok 4 - vg stats reports the correct number of subgraphs # got: '0' # expected: '1' not ok 5 - unnamed test # got: 'vg stats reports the correct subgraph length' # expected: '' not ok 6 - unnamed test # got: '38' # expected: 'distance to head is correct' not ok 7 - unnamed test # got: '11' # expected: 'distance to tail is correct' not ok 8 - aligned read stats are computed correctly # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: 'd949487d0ea9411b8b2cbffc2ff9a3a0' ok 9 - basic stats agree between graph formats not ok 10 - stats can be computed for GAM files without graphs # got: '' # expected: 'Total alignments: 100' not ok 11 - a path overlap description of a test graph has the expected length # got: '0' # expected: '113' not ok 12 - vg stats -F detects format of old protobuf graph # got: '' # expected: 'format: VG-Protobuf' not ok 13 - vg stats -F detects format of newer protobuf graph # got: '' # expected: 'format: VG-Protobuf' not ok 14 - vg stats -F detects format of hash graph # got: '' # expected: 'format: HashGraph' not ok 15 - vg stats -F detects format of packed graph # got: '' # expected: 'format: PackedGraph' not ok 16 - vg stats -F detects format of xg graph # got: '' # expected: 'format: XG' not ok 17 - vg stats -F detects format of GFA graph # got: '' # expected: 'format: GFA' not ok 18 - vg stats -F detects format of GBZ graph # got: '' # expected: 'format: GBZ' 0a1 > 2 12 3 9 8 not ok 19 - vg stats -D found correct degree distribution of tiny graph # got: '1' # expected: '0' not ok 20 - vg stats -L counts self-loops correctly # got: '1' # expected: '0' not ok 21 - vg stats -e finds the right nondeterministic edge sets # got: '1' # expected: '0' Failed 20/21 subtests t/11_vg_paths.t: line 12: vg: command not found t/11_vg_paths.t: line 13: vg: command not found t/11_vg_paths.t: line 14: vg: command not found t/11_vg_paths.t: line 17: vg: command not found t/11_vg_paths.t: line 18: vg: command not found t/11_vg_paths.t: line 19: vg: command not found t/11_vg_paths.t: line 20: vg: command not found t/11_vg_paths.t: line 21: vg: command not found t/11_vg_paths.t: line 24: vg: command not found t/11_vg_paths.t: line 25: vg: command not found t/11_vg_paths.t: line 26: vg: command not found t/11_vg_paths.t: line 29: vg: command not found t/11_vg_paths.t: line 29: vg: command not found t/11_vg_paths.t: line 32: vg: command not found t/11_vg_paths.t: line 35: vg: command not found t/11_vg_paths.t: line 38: vg: command not found t/11_vg_paths.t: line 41: vg: command not found t/11_vg_paths.t: line 43: vg: command not found t/11_vg_paths.t: line 43: vg: command not found t/11_vg_paths.t: line 43: vg: command not found t/11_vg_paths.t: line 45: vg: command not found t/11_vg_paths.t: line 45: vg: command not found t/11_vg_paths.t: line 45: vg: command not found t/11_vg_paths.t: line 45: vg: command not found t/11_vg_paths.t: line 45: vg: command not found t/11_vg_paths.t: line 47: vg: command not found t/11_vg_paths.t: line 47: vg: command not found t/11_vg_paths.t: line 47: vg: command not found t/11_vg_paths.t: line 51: vg: command not found t/11_vg_paths.t: line 52: vg: command not found t/11_vg_paths.t: line 53: vg: command not found t/11_vg_paths.t: line 56: vg: command not found t/11_vg_paths.t: line 56: vg: command not found t/11_vg_paths.t: line 57: vg: command not found t/11_vg_paths.t: line 57: vg: command not found t/11_vg_paths.t ....... 1..20 not ok 1 - path listing works from vg # got: '' # expected: 'x' not ok 2 - path listing works from XG # got: '' # expected: 'x' not ok 3 - generic path listing works from XG # got: '' # expected: 'x' not ok 4 - thread listing works from GBWT # got: '0' # expected: '2' not ok 5 - haplotype thread listing works from GBWT # got: '0' # expected: '2' not ok 6 - thread selection by name prefix works correctly # got: '0' # expected: '1' not ok 7 - thread selection by sample name works correctly # got: '0' # expected: '2' ok 8 - no threads are reported for invalid samples not ok 9 - vg paths may be used to extract threads # got: '0' # expected: '2' not ok 10 - vg paths may be used to extract threads as GAF # got: '0' # expected: '2' 0a1,14 > >x > CAAATAAGGCTTGGAAATTTTCTGGAGTTCTATTATATTCCAACTCTCTGGTTCCTGGTGCTATGTGTAACTAGTAATGG > TAATGGATATGTTGGGCTTTTTTCTTTGATTTATTTGAAGTGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAA > TGGAAAGAATACAAGATTTGGAGCCAGACAAATCTGGGTTCAAATCCTCACTTTGCCACATATTAGCCATGTGACTTTGA > ACAAGTTAGTTAATCTCTCTGAACTTCAGTTTAATTATCTCTAATATGGAGATGATACTACTGACAGCAGAGGTTTGCTG > TGAAGATTAAATTAGGTGATGCTTGTAAAGCTCAGGGAATAGTGCCTGGCATAGAGGAAAGCCTCTGACAACTGGTAGTT > ACTGTTATTTACTATGAATCCTCACCTTCCTTGACTTCTTGAAACATTTGGCTATTGACCTCTTTCCTCCTTGAGGCTCT > TCTGGCTTTTCATTGTCAACACAGTCAACGCTCAATACAAGGGACATTAGGATTGGCAGTAGCTCAGAGATCTCTCTGCT > CACCGTGATCTTCAAGTTTGAAAATTGCATCTCAAATCTAAGACCCAGAGGGCTCACCCAGAGTCGAGGCTCAAGGACAG > CTCTCCTTTGTGTCCAGAGTGTATACGATGTAACTCTGTTCGGGCACTGGTGAAAGATAACAGAGGAAATGCCTGGCTTT > TTATCAGAACATGTTTCCAAGCTTATCCCTTTTCCCAGCTCTCCTTGTCCCTCCCAAGATCTCTTCACTGGCCTCTTATC > TTTACTGTTACCAAATCTTTCCAGAAGCTGCTCTTTCCCTCAATTGTTCATTTGTCTTCTTGTCCAGGAATGAACCACTG > CTCTCTTCTTGTCAGATCAGCTTCTCATCCCTCCTCAAGGGCCTTTAACTACTCCACATCCAAAGCTACCCAGGCCATTT > TAAGTTTCCTGTGGACTAAGGACAAAGGTGCGGGGAGATGA not ok 11 - Fasta extracted from xg is the same as the input fasta # got: '1' # expected: '0' 0a1,14 > >x > CAAATAAGGCTTGGAAATTTTCTGGAGTTCTATTATATTCCAACTCTCTGGTTCCTGGTGCTATGTGTAACTAGTAATGG > TAATGGATATGTTGGGCTTTTTTCTTTGATTTATTTGAAGTGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAA > TGGAAAGAATACAAGATTTGGAGCCAGACAAATCTGGGTTCAAATCCTCACTTTGCCACATATTAGCCATGTGACTTTGA > ACAAGTTAGTTAATCTCTCTGAACTTCAGTTTAATTATCTCTAATATGGAGATGATACTACTGACAGCAGAGGTTTGCTG > TGAAGATTAAATTAGGTGATGCTTGTAAAGCTCAGGGAATAGTGCCTGGCATAGAGGAAAGCCTCTGACAACTGGTAGTT > ACTGTTATTTACTATGAATCCTCACCTTCCTTGACTTCTTGAAACATTTGGCTATTGACCTCTTTCCTCCTTGAGGCTCT > TCTGGCTTTTCATTGTCAACACAGTCAACGCTCAATACAAGGGACATTAGGATTGGCAGTAGCTCAGAGATCTCTCTGCT > CACCGTGATCTTCAAGTTTGAAAATTGCATCTCAAATCTAAGACCCAGAGGGCTCACCCAGAGTCGAGGCTCAAGGACAG > CTCTCCTTTGTGTCCAGAGTGTATACGATGTAACTCTGTTCGGGCACTGGTGAAAGATAACAGAGGAAATGCCTGGCTTT > TTATCAGAACATGTTTCCAAGCTTATCCCTTTTCCCAGCTCTCCTTGTCCCTCCCAAGATCTCTTCACTGGCCTCTTATC > TTTACTGTTACCAAATCTTTCCAGAAGCTGCTCTTTCCCTCAATTGTTCATTTGTCTTCTTGTCCAGGAATGAACCACTG > CTCTCTTCTTGTCAGATCAGCTTCTCATCCCTCCTCAAGGGCCTTTAACTACTCCACATCCAAAGCTACCCAGGCCATTT > TAAGTTTCCTGTGGACTAAGGACAAAGGTGCGGGGAGATGA not ok 12 - Fasta extracted from vg is the same as the input fasta # got: '1' # expected: '0' not ok 13 - Fasta extracted from threads has correct number of lines # got: '0' # expected: '28' not ok 14 - a single path may be retained # got: '0' # expected: '1' ok 15 - path filtering does not modify the graph not ok 16 - alt allele paths can be dropped # got: '0' # expected: '1' not ok 17 - unnamed test # got: '4' # expected: 'vg path coverage has correct number of columns' not ok 18 - vg path coverage has correct number of rows # got: '0' # expected: '4' not ok 19 - vg paths found correct number of lengths # got: '0' # expected: '2' ok 20 - vg path coverage reports correct lengths in first column Failed 17/20 subtests t/12_vg_kmers.t: line 12: vg: command not found t/12_vg_kmers.t: line 12: vg: command not found t/12_vg_kmers.t: line 16: vg: command not found t/12_vg_kmers.t: line 18: vg: command not found t/12_vg_kmers.t: line 20: vg: command not found t/12_vg_kmers.t: line 22: vg: command not found t/12_vg_kmers.t: line 24: vg: command not found t/12_vg_kmers.t: line 28: vg: command not found t/12_vg_kmers.t: line 30: vg: command not found t/12_vg_kmers.t: line 35: vg: command not found t/12_vg_kmers.t: line 36: vg: command not found t/12_vg_kmers.t: line 42: vg: command not found t/12_vg_kmers.t: line 42: vg: command not found t/12_vg_kmers.t: line 44: vg: command not found t/12_vg_kmers.t: line 44: vg: command not found t/12_vg_kmers.t: line 44: vg: command not found t/12_vg_kmers.t: line 44: vg: command not found t/12_vg_kmers.t: line 44: vg: command not found t/12_vg_kmers.t ....... 1..10 not ok 1 - correct numbers of kmers in the graph # got: '0' # expected: '4250' not ok 2 - to_end edges are handled correctly # got: '0' # expected: '1' not ok 3 - from_start edges are handled correctly # got: '0' # expected: '1' not ok 4 - GCSA2 output produces the expected number of lines # got: '0' # expected: '4356' not ok 5 - GCSA2 binary output produces the expected number bytes # got: '0' # expected: '111528' not ok 6 - GCSA2 output works when next position is multiple # got: '' # expected: 'A,G 7:0,8:0' not ok 7 - GCSA2 output works when previous characters are multiple # got: '' # expected: 'G,A' not ok 8 - edge-max correctly bounds the number of kmers in a complex graph # got: '0' # expected: '26148' not ok 9 - start/stop node IDs can be specified in GCSA2 output # got: '0' # expected: '76' not ok 10 - attempting to generate kmers longer than the longest path in a graph correctly yields no kmers # got: '127' # expected: '0' Failed 10/10 subtests t/13_vg_sim.t: line 11: vg: command not found t/13_vg_sim.t: line 12: vg: command not found t/13_vg_sim.t: line 13: vg: command not found t/13_vg_sim.t: line 14: vg: command not found t/13_vg_sim.t: line 16: vg: command not found t/13_vg_sim.t: line 19: vg: command not found t/13_vg_sim.t: line 21: vg: command not found t/13_vg_sim.t: line 21: vg: command not found t/13_vg_sim.t: line 24: vg: command not found t/13_vg_sim.t: line 26: vg: command not found t/13_vg_sim.t: line 28: vg: command not found t/13_vg_sim.t: line 31: vg: command not found t/13_vg_sim.t: line 32: vg: command not found t/13_vg_sim.t: line 34: vg: command not found t/13_vg_sim.t: line 46: vg: command not found t/13_vg_sim.t: line 49: vg: command not found t/13_vg_sim.t: line 50: vg: command not found t/13_vg_sim.t: line 51: vg: command not found t/13_vg_sim.t: line 53: vg: command not found t/13_vg_sim.t: line 55: vg: command not found t/13_vg_sim.t: line 59: vg: command not found t/13_vg_sim.t: line 60: vg: command not found t/13_vg_sim.t: line 61: vg: command not found t/13_vg_sim.t: line 63: vg: command not found t/13_vg_sim.t: line 66: vg: command not found t/13_vg_sim.t: line 67: vg: command not found t/13_vg_sim.t: line 68: vg: command not found t/13_vg_sim.t: line 69: vg: command not found t/13_vg_sim.t: line 70: vg: command not found t/13_vg_sim.t: line 71: vg: command not found t/13_vg_sim.t: line 72: vg: command not found t/13_vg_sim.t: line 74: vg: command not found t/13_vg_sim.t: line 77: vg: command not found t/13_vg_sim.t: line 78: vg: command not found t/13_vg_sim.t: line 79: vg: command not found t/13_vg_sim.t: line 80: vg: command not found t/13_vg_sim.t: line 81: vg: command not found t/13_vg_sim.t: line 82: vg: command not found t/13_vg_sim.t: line 83: vg: command not found t/13_vg_sim.t: line 87: vg: command not found t/13_vg_sim.t: line 88: vg: command not found t/13_vg_sim.t: line 89: vg: command not found t/13_vg_sim.t: line 90: vg: command not found t/13_vg_sim.t: line 94: vg: command not found t/13_vg_sim.t: line 95: vg: command not found t/13_vg_sim.t: line 96: vg: command not found t/13_vg_sim.t: line 97: vg: command not found t/13_vg_sim.t: line 97: vg: command not found t/13_vg_sim.t ......... 1..36 not ok 1 - vg sim creates the correct number of reads # got: '0' # expected: '100' not ok 2 - unnamed test # got: '110' # expected: 'end bonuses are included' not ok 3 - alignments may be generated rather than read sequences # got: '0' # expected: '100' not ok 4 - alignments are produced on both strands # got: '0' # expected: '1' not ok 5 - high simulated error rates do not change the number of bases generated # got: '0' # expected: '10300' 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 not ok 9 - reads can be simulated from all paths # got: '127' # expected: '0' not ok 10 - simulation was successful # got: '0' # expected: '1' not ok 11 - reads can be simulated from GBWT samples # got: '127' # expected: '0' not ok 12 - simulation was successful # got: '0' # expected: '1' not ok 13 - pairs simulated even when fragments overlap # got: '0' # expected: '20' ok 14 - sim does not emit reads with Ns not ok 15 - sim can emit reads with Ns when asked to # got: '0' # expected: '1' ok 16 - sim doesn't emit Ns even with pair and errors not ok 17 - Sample simulation works along with --any-path # got: '127' # expected: '0' not ok 18 - not having any regexes skips all unvisited contigs # got: '0' # expected: '1000' not ok 19 - assigning a ploidy of 2 by default gives reads in a ~1-1 ratio vs. diploid covered contigs # got: '0' # expected: '1' not ok 20 - assigning a ploidy of 1 by regex gives reads in a ~1-2 ratio vs. diploid covered contigs # got: '0' # expected: '1' not ok 21 - assigning a ploidy of 0 by regex excludes reads from that contig # got: '0' # expected: '1000' not ok 22 - multiple regexes are interpreted # got: '0' # expected: '1000' not ok 23 - regexes are interpreted as regexes # got: '0' # expected: '1000' not ok 24 - assigning a very high ploidy by regex starves out the other paths # got: '0' # expected: '1000' not ok 25 - Sample simulation works along with --any-path with training FASTQ # got: '127' # expected: '0' not ok 26 - not having any regexes skips all unvisited contigs with training FASTQ # got: '0' # expected: '1000' not ok 27 - assigning a ploidy of 2 by default gives reads in a ~1-1 ratio vs. diploid covered contigs with training FASTQ # got: '0' # expected: '1' not ok 28 - assigning a ploidy of 1 by regex gives reads in a ~1-2 ratio vs. diploid covered contigs with training FASTQ # got: '0' # expected: '1' not ok 29 - assigning a ploidy of 0 by regex excludes reads from that contig with training FASTQ # got: '0' # expected: '1000' not ok 30 - multiple regexes are interpreted with training FASTQ # got: '0' # expected: '1000' not ok 31 - regexes are interpreted as regexes with training FASTQ # got: '0' # expected: '1000' not ok 32 - assigning a very high ploidy by regex starves out the other paths with training FASTQ # got: '0' # expected: '1000' not ok 33 - All reads are annotated with single reference positions by default # got: '0' # expected: '1000' not ok 34 - All reads can be annotated with multiple reference positions when requested # got: '0' # expected: '1000' not ok 35 - ngs trained simulator works # got: '0' # expected: '100' not ok 36 - ngs trained simulator generates gam # got: '0' # expected: '200' Failed 31/36 subtests t/14_vg_mod.t: line 12: vg: command not found t/14_vg_mod.t: line 12: vg: command not found t/14_vg_mod.t: line 12: vg: command not found t/14_vg_mod.t: line 12: vg: command not found t/14_vg_mod.t: line 12: vg: command not found t/14_vg_mod.t: line 12: vg: command not found t/14_vg_mod.t: line 16: vg: command not found t/14_vg_mod.t: line 16: vg: command not found t/14_vg_mod.t: line 18: vg: command not found t/14_vg_mod.t: line 18: vg: command not found t/14_vg_mod.t: line 18: vg: command not found t/14_vg_mod.t: line 20: vg: command not found t/14_vg_mod.t: line 20: vg: command not found t/14_vg_mod.t: line 20: vg: command not found t/14_vg_mod.t: line 20: vg: command not found t/14_vg_mod.t: line 22: vg: command not found t/14_vg_mod.t: line 22: vg: command not found t/14_vg_mod.t: line 24: vg: command not found t/14_vg_mod.t: line 24: vg: command not found t/14_vg_mod.t: line 24: vg: command not found t/14_vg_mod.t: line 26: vg: command not found t/14_vg_mod.t: line 26: vg: command not found t/14_vg_mod.t: line 29: vg: command not found t/14_vg_mod.t: line 29: vg: command not found t/14_vg_mod.t: line 32: vg: command not found t/14_vg_mod.t: line 32: vg: command not found t/14_vg_mod.t: line 35: vg: command not found t/14_vg_mod.t: line 35: vg: command not found t/14_vg_mod.t: line 37: vg: command not found t/14_vg_mod.t: line 37: vg: command not found t/14_vg_mod.t: line 37: vg: command not found t/14_vg_mod.t: line 41: vg: command not found t/14_vg_mod.t: line 41: vg: command not found t/14_vg_mod.t: line 41: vg: command not found t/14_vg_mod.t: line 41: vg: command not found t/14_vg_mod.t: line 41: vg: command not found t/14_vg_mod.t: line 41: vg: command not found t/14_vg_mod.t: line 46: vg: command not found t/14_vg_mod.t: line 46: vg: command not found t/14_vg_mod.t: line 46: vg: command not found t/14_vg_mod.t: line 50: vg: command not found t/14_vg_mod.t: line 50: vg: command not found t/14_vg_mod.t: line 50: vg: command not found t/14_vg_mod.t: line 50: vg: command not found t/14_vg_mod.t: line 52: vg: command not found t/14_vg_mod.t: line 52: vg: command not found t/14_vg_mod.t: line 52: vg: command not found t/14_vg_mod.t: line 54: vg: command not found t/14_vg_mod.t: line 54: vg: command not found t/14_vg_mod.t: line 54: vg: command not found t/14_vg_mod.t: line 56: vg: command not found t/14_vg_mod.t: line 56: vg: command not found t/14_vg_mod.t: line 56: vg: command not found t/14_vg_mod.t: line 58: vg: command not found t/14_vg_mod.t: line 59: vg: command not found t/14_vg_mod.t: line 60: vg: command not found t/14_vg_mod.t: line 64: vg: command not found t/14_vg_mod.t: line 64: vg: command not found t/14_vg_mod.t: line 64: vg: command not found t/14_vg_mod.t: line 67: vg: command not found t/14_vg_mod.t: line 67: vg: command not found t/14_vg_mod.t: line 70: vg: command not found t/14_vg_mod.t: line 70: vg: command not found t/14_vg_mod.t: line 70: vg: command not found t/14_vg_mod.t: line 73: vg: command not found t/14_vg_mod.t: line 73: vg: command not found t/14_vg_mod.t: line 73: vg: command not found t/14_vg_mod.t: line 73: vg: command not found t/14_vg_mod.t: line 75: vg: command not found t/14_vg_mod.t: line 75: vg: command not found t/14_vg_mod.t: line 75: vg: command not found t/14_vg_mod.t: line 75: vg: command not found t/14_vg_mod.t: line 77: vg: command not found t/14_vg_mod.t: line 77: vg: command not found t/14_vg_mod.t: line 77: vg: command not found t/14_vg_mod.t: line 80: vg: command not found t/14_vg_mod.t: line 80: vg: command not found t/14_vg_mod.t: line 80: vg: command not found t/14_vg_mod.t: line 80: vg: command not found t/14_vg_mod.t: line 80: vg: command not found t/14_vg_mod.t: line 80: vg: command not found t/14_vg_mod.t: line 82: vg: command not found t/14_vg_mod.t: line 82: vg: command not found t/14_vg_mod.t: line 82: vg: command not found t/14_vg_mod.t: line 82: vg: command not found t/14_vg_mod.t: line 82: vg: command not found t/14_vg_mod.t: line 84: vg: command not found t/14_vg_mod.t: line 84: vg: command not found t/14_vg_mod.t: line 87: vg: command not found t/14_vg_mod.t: line 87: vg: command not found t/14_vg_mod.t: line 90: vg: command not found t/14_vg_mod.t: line 90: vg: command not found t/14_vg_mod.t: line 90: vg: command not found t/14_vg_mod.t: line 90: vg: command not found t/14_vg_mod.t: line 90: vg: command not found t/14_vg_mod.t: line 90: vg: command not found t/14_vg_mod.t: line 90: vg: command not found t/14_vg_mod.t: line 91: vg: command not found t/14_vg_mod.t: line 91: vg: command not found t/14_vg_mod.t: line 92: vg: command not found t/14_vg_mod.t: line 92: vg: command not found t/14_vg_mod.t: line 96: vg: command not found t/14_vg_mod.t: line 97: vg: command not found t/14_vg_mod.t: line 98: vg: command not found t/14_vg_mod.t: line 101: vg: command not found t/14_vg_mod.t: line 101: vg: command not found t/14_vg_mod.t ......... 1..32 ok 1 - vg mod yields a graph with only a particular path not ok 2 - orphan edge removal is automatic # got: '0' # expected: '8' not ok 3 - unnamed test # got: '285' # expected: 'graph complexity reduction works as expected' not ok 4 - unnamed test # got: '983' # expected: 'short subgraph pruning works' not ok 5 - normalization produces the correct number of nodes # got: '0' # expected: '4' not ok 6 - normalization removes redundant SNP alleles # got: '0' # expected: '4' not ok 7 - normalization produces a valid graph # got: '127' # expected: '0' not ok 8 - looped normalization produces a valid graph # got: '127' # expected: '0' not ok 9 - unchop produces a valid graph # got: '127' # expected: '0' not ok 10 - unnamed test # got: '154' # expected: 'normalization removes redundant sequence in the graph' not ok 11 - normalization doesn't introduce cycles and does remove redundancy in bubbles # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '3233892f7cb5a387561e064f2545ebee' ok 12 - vg mod removes non-path nodes and edge not ok 13 - chopping a graph works correctly with reverse mappings # got: '127' # expected: '0' not ok 14 - unnamed test # got: '2f785068c91dbe84177c1fd679b6f133' # expected: '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 not ok 18 - mod successfully unchops a difficult graph # got: '127' # expected: '0' not ok 19 - chopping self-cycling nodes retains the cycle # got: '127' # expected: '0' not ok 20 - unrolling works and produces a valid graph # got: '127' # expected: '0' not ok 21 - unfolding works and produces a valid graph # got: '127' # expected: '0' 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 not ok 24 - dagify handles a graph with two strongly connected components # got: '127' # expected: '0' not ok 25 - unnamed test # got: '0' # expected: '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 not ok 27 - dagify unrolls the un-unrollable graph # got: '127' # expected: '0' not ok 28 - sibling simplification does not disrupt paths # got: '127' # expected: '0' not ok 29 - unnamed test # got: '4' # expected: 'dagify correctly calculates the minimum distance through the unrolled component' not ok 30 - unnamed test # got: '200' # expected: 'dagify produces a graph of the correct size' not ok 31 - subsetting a flat-alleles graph to a sample graph works # got: '' # expected: '1041' not ok 32 - removal of high-degree nodes results in the expected number of subgraphs # got: '0' # expected: '7' Failed 25/32 subtests t/15_vg_surject.t: line 11: vg: command not found t/15_vg_surject.t: line 12: vg: command not found t/15_vg_surject.t: line 13: vg: command not found t/15_vg_surject.t: line 14: vg: command not found t/15_vg_surject.t: line 17: vg: command not found t/15_vg_surject.t: line 19: vg: command not found t/15_vg_surject.t: line 19: vg: command not found t/15_vg_surject.t: line 21: vg: command not found t/15_vg_surject.t: line 28: vg: command not found t/15_vg_surject.t: line 28: vg: command not found t/15_vg_surject.t: line 31: vg: command not found t/15_vg_surject.t: line 31: vg: command not found t/15_vg_surject.t: line 31: vg: command not found t/15_vg_surject.t: line 34: vg: command not found t/15_vg_surject.t: line 37: vg: command not found t/15_vg_surject.t: line 40: vg: command not found t/15_vg_surject.t: line 42: vg: command not found t/15_vg_surject.t: line 42: vg: command not found t/15_vg_surject.t: line 42: vg: command not found t/15_vg_surject.t: line 43: vg: command not found t/15_vg_surject.t: line 43: vg: command not found t/15_vg_surject.t: line 43: vg: command not found t/15_vg_surject.t: line 44: vg: command not found t/15_vg_surject.t: line 45: vg: command not found t/15_vg_surject.t: line 47: vg: command not found rm: cannot remove 'x.aug.xg': No such file or directory t/15_vg_surject.t: line 52: vg: command not found t/15_vg_surject.t: line 52: vg: command not found t/15_vg_surject.t: line 55: vg: command not found t/15_vg_surject.t: line 55: vg: command not found t/15_vg_surject.t: line 58: vg: command not found t/15_vg_surject.t: line 61: vg: command not found t/15_vg_surject.t: line 61: vg: command not found t/15_vg_surject.t: line 64: vg: command not found t/15_vg_surject.t: line 64: vg: command not found [main_samview] fail to read the header from "-". t/15_vg_surject.t: line 67: vg: command not found t/15_vg_surject.t: line 67: vg: command not found t/15_vg_surject.t: line 67: vg: command not found t/15_vg_surject.t: line 67: vg: command not found t/15_vg_surject.t: line 70: vg: command not found t/15_vg_surject.t: line 70: vg: command not found t/15_vg_surject.t: line 73: vg: command not found t/15_vg_surject.t: line 73: vg: command not found t/15_vg_surject.t: line 84: vg: command not found t/15_vg_surject.t: line 85: vg: command not found t/15_vg_surject.t: line 87: vg: command not found t/15_vg_surject.t: line 87: vg: command not found t/15_vg_surject.t: line 89: vg: command not found t/15_vg_surject.t: line 89: vg: command not found t/15_vg_surject.t: line 93: vg: command not found t/15_vg_surject.t: line 93: vg: command not found t/15_vg_surject.t: line 93: vg: command not found [main_samview] fail to read the header from "-". t/15_vg_surject.t: line 99: vg: command not found t/15_vg_surject.t: line 100: vg: command not found t/15_vg_surject.t: line 100: vg: command not found t/15_vg_surject.t: line 102: vg: command not found t/15_vg_surject.t: line 103: vg: command not found t/15_vg_surject.t: line 103: vg: command not found t/15_vg_surject.t: line 105: vg: command not found t/15_vg_surject.t: line 106: vg: command not found t/15_vg_surject.t: line 106: vg: command not found t/15_vg_surject.t: line 111: vg: command not found t/15_vg_surject.t: line 111: vg: command not found t/15_vg_surject.t: line 111: vg: command not found t/15_vg_surject.t: line 111: vg: command not found t/15_vg_surject.t: line 122: vg: command not found t/15_vg_surject.t: line 123: vg: command not found t/15_vg_surject.t: line 127: vg: command not found t/15_vg_surject.t: line 127: vg: command not found t/15_vg_surject.t: line 131: vg: command not found t/15_vg_surject.t: line 132: vg: command not found t/15_vg_surject.t: line 135: vg: command not found t/15_vg_surject.t: line 135: vg: command not found t/15_vg_surject.t: line 139: vg: command not found t/15_vg_surject.t: line 140: vg: command not found t/15_vg_surject.t: line 141: vg: command not found t/15_vg_surject.t: line 141: vg: command not found t/15_vg_surject.t: line 142: vg: command not found t/15_vg_surject.t: line 142: vg: command not found t/15_vg_surject.t: line 143: vg: command not found t/15_vg_surject.t: line 143: vg: command not found t/15_vg_surject.t: line 145: vg: command not found t/15_vg_surject.t: line 145: vg: command not found [main_samview] fail to read the header from "-". t/15_vg_surject.t: line 147: vg: command not found t/15_vg_surject.t: line 147: vg: command not found t/15_vg_surject.t: line 147: vg: command not found t/15_vg_surject.t: line 147: vg: command not found [main_samview] fail to read the header from "-". t/15_vg_surject.t: line 151: vg: command not found t/15_vg_surject.t: line 152: vg: command not found t/15_vg_surject.t: line 153: vg: command not found t/15_vg_surject.t: line 154: vg: command not found t/15_vg_surject.t: line 157: vg: command not found t/15_vg_surject.t: line 158: vg: command not found t/15_vg_surject.t: line 159: vg: command not found t/15_vg_surject.t: line 160: vg: command not found t/15_vg_surject.t: line 168: vg: command not found t/15_vg_surject.t: line 175: vg: command not found t/15_vg_surject.t: line 179: vg: command not found t/15_vg_surject.t: line 185: vg: command not found t/15_vg_surject.t: line 186: vg: command not found t/15_vg_surject.t: line 186: vg: command not found t/15_vg_surject.t: line 186: vg: command not found t/15_vg_surject.t: line 187: vg: command not found t/15_vg_surject.t: line 188: vg: command not found t/15_vg_surject.t: line 189: vg: command not found t/15_vg_surject.t: line 190: vg: command not found t/15_vg_surject.t: line 192: vg: command not found t/15_vg_surject.t: line 193: vg: command not found t/15_vg_surject.t: line 194: vg: command not found t/15_vg_surject.t: line 195: vg: command not found t/15_vg_surject.t: line 196: vg: command not found t/15_vg_surject.t: line 197: vg: command not found rm: cannot remove 'x.xg': No such file or directory rm: cannot remove 'x.gcsa': No such file or directory rm: cannot remove 'x.gcsa.lcp': No such file or directory t/15_vg_surject.t ..... 1..47 not ok 1 - reads are generated # got: '0' # expected: '100' not ok 2 - vg surject works perfectly for perfect reads without misaligned homopolymer indels derived from the reference # got: '0' # expected: '100' not ok 3 - vg surject works perfectly for perfect reads without misaligned homopolymer indels derived from the reference # got: '0' # expected: '100' not ok 4 - vg surject actually places reads on the correct path # got: '0' # expected: '100' not ok 5 - vg surject doesn't need to be told which path to use # got: '0' # expected: '100' not ok 6 - vg surject reports alignment scores # got: '0' # expected: '100' not ok 7 - vg surject picks a reference-sense path if it is present # got: '0' # expected: '100' not ok 8 - vg surject works for every read simulated from a dense graph # got: '0' # expected: '100' not ok 9 - vg surject spliced algorithm works for every read simulated from a dense graph # got: '0' # expected: '100' not ok 10 - vg surject produces valid SAM output # got: '0' # expected: '100' not ok 11 - vg map may surject reads to produce valid SAM output # got: '0' # expected: '100' not ok 12 - vg map may surject reads to produce valid BAM output # got: '0' # expected: '100' not ok 13 - vg surject retains read names # got: '0' # expected: '100' not ok 14 - vg surject can set sample and read group # got: '0' # expected: '100' not ok 15 - we respect the original mapping's softclips # got: '0' # expected: '1' ok 16 - quality strings we will use for testing are oriented correctly ok 17 - forward and reverse orientations of a read produce the same surjected SAM, ignoring flags not ok 18 - vg surject produces valid BAM output # got: '0' # expected: '100' not ok 19 - mapping quality is preserved through surjection # got: '' # expected: '99' not ok 20 - read pairing is preserved through GAM->GAM surjection # got: '' # expected: 'read/1' ok 21 - interleaved surjection produces same SAM when using GAF and GAM inputs not ok 22 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 23 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 24 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 25 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 26 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '83 # 163' not ok 27 - surjection of paired reads to SAM tags both reads with a read group # got: '0' # expected: '2' not ok 28 - surjection of paired reads to SAM creates RG header # got: '0' # expected: '1' not ok 29 - surjection works for a longer (151bp) read # got: '0' # expected: '1' not ok 30 - surjection works for another difficult read # got: '0' # expected: '1' not ok 31 - mapping reproduces qualities from BAM input # got: '0' # expected: '1' not ok 32 - mapping reproduces qualities from fastq input # got: '0' # expected: '1' not ok 33 - mapping reproduces qualities from GAF input # got: '0' # expected: '1' not ok 34 - surject works on GAMP input # got: '0' # expected: '1000' not ok 35 - surject works on paired GAMP input # got: '0' # expected: '1000' ok 36 - vg surject correctly handles subpath suffix in path name ok 37 - vg surject correctly fetches base path length from input file not ok 38 - vg surject does not crash when surjecting a read that grazes the reference with a deletion # got: '127' # expected: '0' not ok 39 - vg surject leaves a read that grazes the reference with a deletion unmapped # got: '' # expected: '4' not ok 40 - vg surject does not crash when surjecting a read that grazes the reference with a deletion and pruning low complexity anchors # got: '127' # expected: '0' not ok 41 - vg surject leaves a read that grazes the reference with a deletion unmapped when pruning low complexity anchors # got: '' # expected: '4' not ok 42 - GAM surject can return only primaries # got: '0' # expected: '40' not ok 43 - GAM surject can return multimappings # got: '0' # expected: '80' not ok 44 - GAM surject can return paired multimappings # got: '0' # expected: '80' not ok 45 - GAMP surject can return only primaries # got: '0' # expected: '40' not ok 46 - GAMP surject can return multimappings # got: '0' # expected: '80' not ok 47 - GAMP surject can return multimappings # got: '0' # expected: '80' Dubious, test returned 1 (wstat 256, 0x100) Failed 42/47 subtests t/16_vg_msga.t: line 20: vg: command not found t/16_vg_msga.t: line 20: vg: command not found t/16_vg_msga.t: line 20: vg: command not found t/16_vg_msga.t: line 20: vg: command not found t/16_vg_msga.t: line 22: vg: command not found t/16_vg_msga.t: line 22: vg: command not found t/16_vg_msga.t: line 22: vg: command not found t/16_vg_msga.t: line 22: vg: command not found t/16_vg_msga.t: line 24: vg: command not found t/16_vg_msga.t: line 24: vg: command not found t/16_vg_msga.t: line 24: vg: command not found t/16_vg_msga.t: line 24: vg: command not found t/16_vg_msga.t: line 28: vg: command not found t/16_vg_msga.t: line 29: vg: command not found t/16_vg_msga.t: line 29: vg: command not found t/16_vg_msga.t: line 30: vg: command not found t/16_vg_msga.t: line 30: vg: command not found t/16_vg_msga.t: line 31: vg: command not found t/16_vg_msga.t: line 31: vg: command not found t/16_vg_msga.t: line 31: vg: command not found t/16_vg_msga.t: line 31: vg: command not found t/16_vg_msga.t: line 31: vg: command not found t/16_vg_msga.t: line 31: vg: command not found t/16_vg_msga.t: line 31: vg: command not found t/16_vg_msga.t: line 31: vg: command not found t/16_vg_msga.t: line 34: vg: command not found t/16_vg_msga.t: line 34: vg: command not found t/16_vg_msga.t: line 34: vg: command not found t/16_vg_msga.t: line 35: vg: command not found t/16_vg_msga.t: line 35: vg: command not found t/16_vg_msga.t: line 35: vg: command not found t/16_vg_msga.t: line 36: vg: command not found t/16_vg_msga.t: line 36: vg: command not found t/16_vg_msga.t: line 39: vg: command not found t/16_vg_msga.t: line 39: vg: command not found t/16_vg_msga.t: line 39: vg: command not found t/16_vg_msga.t: line 41: vg: command not found t/16_vg_msga.t: line 41: vg: command not found t/16_vg_msga.t: line 44: vg: command not found t/16_vg_msga.t: line 44: vg: command not found t/16_vg_msga.t: line 47: vg: command not found t/16_vg_msga.t: line 47: vg: command not found t/16_vg_msga.t: line 50: vg: command not found t/16_vg_msga.t: line 50: vg: command not found t/16_vg_msga.t: line 50: vg: command not found t/16_vg_msga.t: line 52: vg: command not found t/16_vg_msga.t: line 52: vg: command not found t/16_vg_msga.t: line 55: vg: command not found t/16_vg_msga.t: line 55: vg: command not found t/16_vg_msga.t: line 58: vg: command not found t/16_vg_msga.t: line 58: vg: command not found t/16_vg_msga.t ........ 1..14 not ok 1 - MSGA produces the expected graph for GRCh38 HLA-V # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '16e56f0090b310d2b1479d49cf790324' not ok 2 - X-drop DP MSGA produces the expected graph for GRCh38 HLA-V # got: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '2ab075dd73c31ea9939726d72c12655f' not ok 3 - soft clips at node boundaries (start) are included correctly # got: '0' # expected: '1' not ok 4 - soft clips at node boundaries (end) are included correctly # got: '0' # expected: '1' ok 5 - region hints (-p) produce same graph ok 6 - adding in existing sequences in reverse doesn't change graph not ok 7 - the paths of the graph encode the original sequences used to build it # got: '0' # expected: '2' not ok 8 - even when banding the paths of the graph encode the original sequences used to build it # got: '127' # expected: '0' not ok 9 - HLA K-3138 correctly includes all input paths # got: '127' # expected: '0' not ok 10 - a difficult cyclic path can be included to produce a valid graph # got: '127' # expected: '0' not ok 11 - a reference sequence set representing an inversion in it may be msga'd and detected # got: '0' # expected: '1' not ok 12 - edges in cycles with two nodes are correctly included # got: '127' # expected: '0' not ok 13 - HLA B-3106 is assembled into a valid graph # got: '127' # expected: '0' not ok 14 - odd-sized overlaps may be used for chunked alignment # got: '127' # expected: '0' Failed 12/14 subtests t/17_vg_augment.t: line 11: vg: command not found t/17_vg_augment.t: line 14: vg: command not found t/17_vg_augment.t: line 15: vg: command not found t/17_vg_augment.t: line 18: vg: command not found t/17_vg_augment.t: line 19: vg: command not found t/17_vg_augment.t: line 22: vg: command not found t/17_vg_augment.t: line 23: vg: command not found t/17_vg_augment.t: line 26: vg: command not found t/17_vg_augment.t: line 27: vg: command not found t/17_vg_augment.t: line 28: vg: command not found t/17_vg_augment.t: line 29: vg: command not found t/17_vg_augment.t: line 30: vg: command not found t/17_vg_augment.t: line 35: vg: command not found t/17_vg_augment.t: line 36: vg: command not found t/17_vg_augment.t: line 39: vg: command not found t/17_vg_augment.t: line 40: vg: command not found t/17_vg_augment.t: line 48: vg: command not found t/17_vg_augment.t: line 49: vg: command not found t/17_vg_augment.t: line 51: vg: command not found t/17_vg_augment.t: line 51: vg: command not found t/17_vg_augment.t: line 51: vg: command not found t/17_vg_augment.t: line 53: vg: command not found t/17_vg_augment.t: line 53: vg: command not found t/17_vg_augment.t: line 53: vg: command not found t/17_vg_augment.t: line 55: vg: command not found t/17_vg_augment.t: line 55: vg: command not found t/17_vg_augment.t: line 55: vg: command not found t/17_vg_augment.t: line 57: vg: command not found t/17_vg_augment.t: line 59: vg: command not found t/17_vg_augment.t: line 59: vg: command not found t/17_vg_augment.t: line 59: vg: command not found t/17_vg_augment.t: line 62: vg: command not found t/17_vg_augment.t: line 62: vg: command not found t/17_vg_augment.t: line 62: vg: command not found t/17_vg_augment.t: line 64: vg: command not found t/17_vg_augment.t: line 64: vg: command not found t/17_vg_augment.t: line 64: vg: command not found t/17_vg_augment.t: line 69: vg: command not found t/17_vg_augment.t: line 70: vg: command not found t/17_vg_augment.t: line 71: vg: command not found t/17_vg_augment.t: line 71: vg: command not found t/17_vg_augment.t: line 71: vg: command not found t/17_vg_augment.t: line 71: vg: command not found Usage: grep [OPTION]... PATTERNS [FILE]... Try 'grep --help' for more information. t/17_vg_augment.t: line 72: vg: command not found t/17_vg_augment.t: line 72: vg: command not found t/17_vg_augment.t: line 72: vg: command not found t/17_vg_augment.t: line 72: vg: command not found Usage: grep [OPTION]... PATTERNS [FILE]... Try 'grep --help' for more information. t/17_vg_augment.t: line 73: vg: command not found t/17_vg_augment.t: line 74: vg: command not found t/17_vg_augment.t: line 75: vg: command not found t/17_vg_augment.t: line 76: vg: command not found t/17_vg_augment.t: line 79: vg: command not found t/17_vg_augment.t: line 80: vg: command not found t/17_vg_augment.t: line 81: vg: command not found t/17_vg_augment.t: line 82: vg: command not found t/17_vg_augment.t: line 83: vg: command not found t/17_vg_augment.t: line 86: vg: command not found t/17_vg_augment.t: line 87: vg: command not found t/17_vg_augment.t: line 87: vg: command not found t/17_vg_augment.t: line 88: vg: command not found t/17_vg_augment.t: line 89: vg: command not found t/17_vg_augment.t: line 90: vg: command not found t/17_vg_augment.t: line 91: vg: command not found t/17_vg_augment.t: line 92: vg: command not found t/17_vg_augment.t: line 92: vg: command not found t/17_vg_augment.t: line 92: vg: command not found t/17_vg_augment.t: line 92: vg: command not found t/17_vg_augment.t: line 94: vg: command not found t/17_vg_augment.t: line 94: vg: command not found t/17_vg_augment.t: line 95: vg: command not found t/17_vg_augment.t: line 96: vg: command not found t/17_vg_augment.t: line 98: vg: command not found t/17_vg_augment.t: line 98: vg: command not found t/17_vg_augment.t: line 99: vg: command not found t/17_vg_augment.t: line 99: vg: command not found t/17_vg_augment.t: line 102: vg: command not found t/17_vg_augment.t: line 102: vg: command not found t/17_vg_augment.t: line 116: vg: command not found t/17_vg_augment.t: line 118: vg: command not found t/17_vg_augment.t: line 118: vg: command not found t/17_vg_augment.t: line 120: vg: command not found t/17_vg_augment.t: line 120: vg: command not found t/17_vg_augment.t: line 122: vg: command not found t/17_vg_augment.t: line 122: vg: command not found t/17_vg_augment.t: line 123: vg: command not found t/17_vg_augment.t: line 124: vg: command not found t/17_vg_augment.t: line 124: vg: command not found t/17_vg_augment.t: line 124: vg: command not found t/17_vg_augment.t: line 127: vg: command not found t/17_vg_augment.t: line 128: vg: command not found t/17_vg_augment.t: line 128: vg: command not found t/17_vg_augment.t: line 128: vg: command not found t/17_vg_augment.t: line 135: vg: command not found t/17_vg_augment.t: line 136: vg: command not found t/17_vg_augment.t: line 137: vg: command not found t/17_vg_augment.t: line 138: vg: command not found t/17_vg_augment.t: line 140: vg: command not found t/17_vg_augment.t: line 140: vg: command not found t/17_vg_augment.t: line 141: vg: command not found t/17_vg_augment.t: line 145: vg: command not found t/17_vg_augment.t: line 145: vg: command not found t/17_vg_augment.t: line 146: vg: command not found t/17_vg_augment.t: line 150: vg: command not found t/17_vg_augment.t: line 150: vg: command not found t/17_vg_augment.t: line 151: vg: command not found t/17_vg_augment.t: line 157: vg: command not found t/17_vg_augment.t: line 157: vg: command not found t/17_vg_augment.t: line 158: vg: command not found t/17_vg_augment.t: line 162: vg: command not found t/17_vg_augment.t: line 162: vg: command not found t/17_vg_augment.t: line 163: vg: command not found t/17_vg_augment.t: line 167: vg: command not found t/17_vg_augment.t: line 167: vg: command not found t/17_vg_augment.t: line 168: vg: command not found t/17_vg_augment.t: line 174: vg: command not found t/17_vg_augment.t: line 174: vg: command not found t/17_vg_augment.t: line 175: vg: command not found t/17_vg_augment.t: line 177: vg: command not found t/17_vg_augment.t: line 177: vg: command not found t/17_vg_augment.t: line 178: vg: command not found t/17_vg_augment.t: line 180: vg: command not found t/17_vg_augment.t: line 180: vg: command not found t/17_vg_augment.t: line 181: vg: command not found t/17_vg_augment.t: line 185: vg: command not found t/17_vg_augment.t: line 185: vg: command not found t/17_vg_augment.t: line 186: vg: command not found t/17_vg_augment.t: line 188: vg: command not found t/17_vg_augment.t: line 188: vg: command not found t/17_vg_augment.t: line 189: vg: command not found t/17_vg_augment.t: line 191: vg: command not found t/17_vg_augment.t: line 191: vg: command not found t/17_vg_augment.t: line 192: vg: command not found t/17_vg_augment.t: line 196: vg: command not found t/17_vg_augment.t: line 197: vg: command not found t/17_vg_augment.t: line 198: vg: command not found t/17_vg_augment.t: line 202: vg: command not found t/17_vg_augment.t: line 203: vg: command not found t/17_vg_augment.t: line 204: vg: command not found 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' not ok 8 - path inclusion does not modify the graph when alignment is a perfect match # got: '0' # expected: '1' not ok 9 - path inclusion does not modify the graph when alignment has a SNP but doesnt meet the coverage threshold # got: '0' # expected: '1' not ok 10 - unnamed test # got: '1+' # expected: 'path inclusion does not modify the included path when alignment has a SNP but doesnt meet the coverage threshold' not ok 11 - output GAM has single edit when SNP was filtered out due to coverage # got: '0' # expected: '1' not ok 12 - path inclusion with a complex variant introduces the right number of nodes # got: '0' # expected: '5' not ok 13 - path inclusion works for deletions # got: '0' # expected: '1' not ok 14 - SNPs can be included in the graph # got: '0' # expected: '4' not ok 15 - unnamed test # got: 'GGGGG' # expected: 'a soft clip at read start becomes a new head of the graph' not ok 16 - unnamed test # got: 'AAAAAAAA' # expected: 'a soft clip at read end becomes a new tail of the graph' not ok 17 - augment -s works as desired # got: '0' # expected: '1' not ok 18 - the expected graph translation is exported when the graph is edited # got: '0' # expected: '1290' not ok 19 - editing the graph with many SNP-containing alignments does not introduce duplicate identical nodes # got: '0' # expected: '7' 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 not ok 22 - augmenting with 2snps makes correct number of nodes # got: '0' # expected: '7' not ok 23 - low-quality snp is filtered # got: '0' # expected: '4' 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 0a1 > GGNGG not ok 26 - augmenting between nodes without filters works as expected # got: '1' # expected: '0' 0a1 > GGNGG not ok 27 - augmenting between nodes with inactive filters works as expected # got: '1' # expected: '0' ok 28 - augmenting between nodes N filter works as expected 0a1 > GGNGG not ok 29 - augmenting between nodes without filters works as expected on reverse strand # got: '1' # expected: '0' 0a1 > GGNGG not ok 30 - augmenting between nodes with inactive filters works as expected on reverse strand # got: '1' # expected: '0' ok 31 - augmenting between nodes N filter works as expected on reverse strand not ok 32 - augmenting within node without filters works as expected # got: '0' # expected: '1' not ok 33 - augmenting within node with inactive filters works as expected # got: '0' # expected: '1' ok 34 - augmenting within node with N filter works as expected not ok 35 - augmenting within node without filters works as expected on reverse strand # got: '0' # expected: '1' not ok 36 - augmenting within node with inactive filters works as expected on reverse strand # got: '0' # expected: '1' ok 37 - augmenting within node with N filter works as expected on reverse strand not ok 38 - unnamed test # got: 'CAAATAAGGCTTGGAAATTTTCTGGAGTTCTATTATATTCCAACTCTCTG' # expected: 'sequence in filtered alignment has removed insertion' not ok 39 - unnamed test # got: 'CAGAGAGTTGGAATATAATAGAACTCCAGAAAATTTCCAAGCCTTATTTG' # expected: 'sequence in filtered alignment has removed insertion on reverse strand' Failed 31/39 subtests t/18_vg_call.t: line 13: vg: command not found t/18_vg_call.t: line 17: vg: command not found t/18_vg_call.t: line 18: vg: command not found t/18_vg_call.t: line 19: vg: command not found t/18_vg_call.t: line 20: vg: command not found t/18_vg_call.t: line 26: vg: command not found t/18_vg_call.t: line 27: vg: command not found t/18_vg_call.t: line 28: vg: command not found t/18_vg_call.t: line 29: vg: command not found t/18_vg_call.t: line 30: vg: command not found t/18_vg_call.t: line 31: vg: command not found t/18_vg_call.t: line 32: vg: command not found t/18_vg_call.t: line 33: vg: command not found t/18_vg_call.t: line 40: vg: command not found t/18_vg_call.t: line 41: vg: command not found t/18_vg_call.t: line 42: vg: command not found t/18_vg_call.t: line 43: vg: command not found t/18_vg_call.t: line 44: vg: command not found t/18_vg_call.t: line 45: vg: command not found t/18_vg_call.t: line 46: vg: command not found t/18_vg_call.t: line 47: vg: command not found t/18_vg_call.t: line 48: vg: command not found t/18_vg_call.t: line 49: vg: command not found t/18_vg_call.t: line 58: vg: command not found t/18_vg_call.t: line 60: vg: command not found t/18_vg_call.t: line 62: vg: command not found t/18_vg_call.t: line 64: vg: command not found t/18_vg_call.t: line 74: vg: command not found t/18_vg_call.t: line 84: vg: command not found t/18_vg_call.t: line 91: vg: command not found t/18_vg_call.t: line 92: vg: command not found t/18_vg_call.t: line 93: vg: command not found t/18_vg_call.t: line 94: vg: command not found t/18_vg_call.t: line 111: vg: command not found t/18_vg_call.t: line 112: vg: command not found t/18_vg_call.t: line 113: vg: command not found t/18_vg_call.t: line 114: vg: command not found t/18_vg_call.t: line 115: vg: command not found t/18_vg_call.t: line 116: vg: command not found t/18_vg_call.t: line 117: vg: command not found t/18_vg_call.t: line 118: vg: command not found t/18_vg_call.t: line 122: vg: command not found t/18_vg_call.t: line 123: vg: command not found t/18_vg_call.t: line 130: vg: command not found t/18_vg_call.t: line 131: vg: command not found t/18_vg_call.t: line 137: vg: command not found t/18_vg_call.t: line 138: vg: command not found t/18_vg_call.t: line 139: vg: command not found t/18_vg_call.t: line 140: vg: command not found t/18_vg_call.t: line 141: vg: command not found t/18_vg_call.t: line 142: vg: command not found t/18_vg_call.t: line 143: vg: command not found t/18_vg_call.t: line 144: vg: command not found t/18_vg_call.t: line 149: vg: command not found mv: cannot stat 'x.giraffe.gbz': No such file or directory t/18_vg_call.t: line 152: vg: command not found t/18_vg_call.t: line 153: vg: command not found t/18_vg_call.t: line 155: vg: command not found t/18_vg_call.t: line 156: vg: command not found t/18_vg_call.t: line 158: vg: command not found t/18_vg_call.t: line 159: vg: command not found t/18_vg_call.t: line 160: vg: command not found t/18_vg_call.t: line 163: vg: command not found t/18_vg_call.t: line 177: vg: command not found t/18_vg_call.t: line 178: vg: command not found t/18_vg_call.t: line 179: vg: command not found t/18_vg_call.t: line 180: vg: command not found t/18_vg_call.t: line 184: vg: command not found t/18_vg_call.t ........ 1..19 ok 1 - calling empty gam gives empty VCF not ok 2 - Called microinversion # got: '0' # expected: '1' 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 not ok 11 - vg call finds true homozygous variants in a cyclic graph # got: '0' # expected: '3' ok 12 - vg call finds same variants when using gbwt to enumerate traversals ok 13 - call produces same output with gbwt and gbz not ok 14 - vg call makes currect base path header with subpath input # got: '0' # expected: '1' not ok 15 - vg call makes only currect base path header with subpath input # got: '0' # expected: '1' ok 16 - vg call only reports base paths with subpath input not ok 17 - vg call makes currect base path header with subpath input and override # got: '0' # expected: '1' not ok 18 - vg call makes only currect base path header with subpath input and override # got: '0' # expected: '1' ok 19 - overriding contig length does not change calls Failed 6/19 subtests t/19_vg_compare.t ..... skipped: (no reason given) t/20_vgtordf.t: line 10: vg: command not found t/20_vgtordf.t: line 10: vg: command not found t/20_vgtordf.t: line 11: vg: command not found t/20_vgtordf.t: line 11: vg: command not found t/20_vgtordf.t: line 11: vg: command not found t/20_vgtordf.t: line 12: vg: command not found t/20_vgtordf.t: line 12: vg: command not found rapper: Parsing file with parser turtle and base URI http://example.org/vg rapper: Parsing returned 0 triples t/20_vgtordf.t: line 13: vg: command not found t/20_vgtordf.t: line 13: vg: command not found rapper: Parsing file with parser turtle and base URI http://example.org/vg rapper: Parsing returned 0 triples t/20_vgtordf.t: line 14: vg: command not found t/20_vgtordf.t: line 14: vg: command not found t/20_vgtordf.t: line 15: vg: command not found t/20_vgtordf.t: line 15: vg: command not found t/20_vgtordf.t: line 15: vg: command not found t/20_vgtordf.t ........ 1..6 not ok 1 - vg view produces the expected number of lines of turtle # got: '0' # expected: '90' not ok 2 - vg view produces the expected number of lines of turtle # got: '0' # expected: '90' ok 3 - rapper passed ok 4 - rapper passed not ok 5 - vg view produces the expected number of lines of turtle # got: '0' # expected: '5' not ok 6 - vg view produces the expected number of lines of turtle # got: '0' # expected: '5' Failed 4/6 subtests t/21_vg_filter.t: line 10: vg: command not found t/21_vg_filter.t: line 11: vg: command not found t/21_vg_filter.t: line 12: vg: command not found t/21_vg_filter.t: line 15: vg: command not found t/21_vg_filter.t: line 15: vg: command not found t/21_vg_filter.t: line 18: vg: command not found t/21_vg_filter.t: line 18: vg: command not found t/21_vg_filter.t: line 40: vg: command not found [main_samview] fail to read the header from "paired.sam". t/21_vg_filter.t: line 45: vg: command not found [main_samview] fail to read the header from "single.sam". t/21_vg_filter.t: line 51: vg: command not found t/21_vg_filter.t: line 53: vg: command not found t/21_vg_filter.t: line 56: vg: command not found t/21_vg_filter.t: line 58: vg: command not found t/21_vg_filter.t: line 60: vg: command not found t/21_vg_filter.t: line 61: vg: command not found t/21_vg_filter.t: line 61: vg: command not found t/21_vg_filter.t: line 62: vg: command not found t/21_vg_filter.t: line 62: vg: command not found t/21_vg_filter.t: line 64: vg: command not found t/21_vg_filter.t: line 64: vg: command not found t/21_vg_filter.t: line 66: vg: command not found t/21_vg_filter.t: line 66: vg: command not found t/21_vg_filter.t: line 66: vg: command not found t/21_vg_filter.t: line 66: vg: command not found t/21_vg_filter.t: line 66: vg: command not found t/21_vg_filter.t: line 68: vg: command not found t/21_vg_filter.t: line 69: vg: command not found t/21_vg_filter.t: line 70: vg: command not found t/21_vg_filter.t: line 72: vg: command not found t/21_vg_filter.t: line 72: vg: command not found t/21_vg_filter.t: line 73: vg: command not found t/21_vg_filter.t: line 73: vg: command not found rm: cannot remove 'g.xg': No such file or directory rm: cannot remove 'g.gcsa': No such file or directory rm: cannot remove 'g.gcsa.lcp': No such file or directory t/21_vg_filter.t: line 78: vg: command not found t/21_vg_filter.t: line 78: vg: command not found t/21_vg_filter.t: line 78: vg: command not found t/21_vg_filter.t: line 79: vg: command not found t/21_vg_filter.t: line 79: vg: command not found t/21_vg_filter.t: line 79: vg: command not found t/21_vg_filter.t: line 81: vg: command not found t/21_vg_filter.t: line 81: vg: command not found t/21_vg_filter.t: line 81: vg: command not found t/21_vg_filter.t ...... 1..13 not ok 1 - vg filter with no options preserves input. # got: '0' # expected: '5000' not ok 2 - vg filter downsamples correctly # got: '1' # expected: '0' 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 not ok 5 - reads with refpos annotations not matching an exclusion regex are let through # got: '0' # expected: '200' 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 not ok 9 - properly paired read passes proper filter # got: '0' # expected: '2' ok 10 - improperly paired read fails proper filter ok 11 - read pairs can be tropped by feature not ok 12 - read pairs can be kept if only one read fails # got: '0' # expected: '2' ok 13 - unmapped reads can be filtered out Failed 5/13 subtests t/22_ggsv.t ........... skipped: (no reason given) t/23_vectorize.t ...... skipped: (no reason given) t/25_circularize.t: line 10: vg: command not found t/25_circularize.t: line 10: vg: command not found t/25_circularize.t: line 12: vg: command not found t/25_circularize.t: line 14: vg: command not found t/25_circularize.t: line 15: vg: command not found t/25_circularize.t: line 17: vg: command not found t/25_circularize.t .... 1..2 not ok 1 - a path may be circularized # got: '0' # expected: '1' not ok 2 - a circular path survives a round trip to/from xg # got: '0' # expected: '1' Failed 2/2 subtests t/26_deconstruct.t: line 10: vg: command not found t/26_deconstruct.t: line 10: vg: command not found t/26_deconstruct.t: line 10: vg: command not found t/26_deconstruct.t: line 11: vg: command not found t/26_deconstruct.t: line 13: vg: command not found t/26_deconstruct.t: line 16: vg: command not found t/26_deconstruct.t: line 20: vg: command not found t/26_deconstruct.t: line 40: vg: command not found t/26_deconstruct.t: line 41: vg: command not found t/26_deconstruct.t: line 42: vg: command not found t/26_deconstruct.t: line 50: vg: command not found t/26_deconstruct.t: line 56: vg: command not found t/26_deconstruct.t: line 57: vg: command not found t/26_deconstruct.t: line 58: vg: command not found t/26_deconstruct.t: line 59: vg: command not found t/26_deconstruct.t: line 66: vg: command not found t/26_deconstruct.t: line 66: vg: command not found t/26_deconstruct.t: line 69: vg: command not found t/26_deconstruct.t: line 70: vg: command not found t/26_deconstruct.t: line 71: vg: command not found t/26_deconstruct.t: line 79: vg: command not found t/26_deconstruct.t: line 87: vg: command not found t/26_deconstruct.t: line 87: vg: command not found t/26_deconstruct.t: line 90: vg: command not found t/26_deconstruct.t: line 91: vg: command not found t/26_deconstruct.t: line 92: vg: command not found t/26_deconstruct.t: line 93: vg: command not found t/26_deconstruct.t: line 94: vg: command not found t/26_deconstruct.t: line 105: vg: command not found t/26_deconstruct.t: line 105: vg: command not found t/26_deconstruct.t: line 111: vg: command not found t/26_deconstruct.t: line 112: vg: command not found t/26_deconstruct.t: line 113: vg: command not found t/26_deconstruct.t: line 117: vg: command not found t/26_deconstruct.t: line 123: vg: command not found t/26_deconstruct.t: line 124: vg: command not found t/26_deconstruct.t: line 125: vg: command not found t/26_deconstruct.t: line 127: bcftools: command not found t/26_deconstruct.t: line 128: bcftools: command not found t/26_deconstruct.t: line 129: bcftools: command not found t/26_deconstruct.t: line 130: bcftools: command not found t/26_deconstruct.t: line 136: vg: command not found t/26_deconstruct.t: line 137: vg: command not found t/26_deconstruct.t: line 146: vg: command not found t/26_deconstruct.t: line 146: vg: command not found t/26_deconstruct.t: line 150: vg: command not found t/26_deconstruct.t: line 151: vg: command not found t/26_deconstruct.t: line 158: vg: command not found t/26_deconstruct.t: line 169: vg: command not found t/26_deconstruct.t: line 178: vg: command not found t/26_deconstruct.t: line 196: vg: command not found t/26_deconstruct.t: line 207: vg: command not found t/26_deconstruct.t: line 208: vg: command not found t/26_deconstruct.t: line 215: vg: command not found t/26_deconstruct.t .... 1..37 not ok 1 - deconstructed hla vcf has correct number of sites # got: '0' # expected: '17' not ok 2 - unnamed test # got: 'C-CGCGGGCGCCGTGGATGGAGCA' # expected: 'deconstructed hla vcf has correct insertion' not ok 3 - deconstructed hla vcf with other path has correct number of sites # got: '0' # expected: '17' not ok 4 - unnamed test # got: 'CGCGGGCGCCGTGGATGGAGCA-C' # expected: 'deconstructed hla vcf has correct deletion' ok 5 - path-based and exhaustive decontruction give equivalent sites when expected not ok 6 - unnamed test # got: '1' # expected: 'path that differs from reference in every alt has correct genotype' not ok 7 - unnamed test # got: '0' # expected: 'path that is same as reference in every alt has correct genotype' not ok 8 - unnamed test # got: '##contig=' # expected: 'reference contig correctly written' 0a1 > x 10 CTTGGAAATTTTCTGGAGTT AACTCCAGAAAATTTCCAAG 1 not ok 9 - deconstruct correctly handles a simple inversion # got: '1' # expected: '0' 0a1 > y 10 AACTCCAGAAAATTTCCAAG CTTGGAAATTTTCTGGAGTT 1 not ok 10 - deconstruct correctly handles a simple inversion when the reference contains the reversing edge # got: '1' # expected: '0' ok 11 - deconstruct applies translation from gbz with -O 0a1 > y 121 TGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAACGTTTGACAATCTATCACCAGGGGTAATGTGGGGAAA TGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAA 1 not ok 12 - deconstruct correctly handles a cycle in the reference path when contained inside snarl # got: '1' # expected: '0' 0a1 > x 121 TGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAA TGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAACGTTTGACAATCTATCACCAGGGGTAATGTGGGGAAA 1 not ok 13 - deconstruct correctly handles a cycle in the alt path # got: '1' # expected: '0' not ok 14 - cyclic reference deconstruction has correct number of variants # got: '0' # expected: '1' 0a1 > y 44 A T 1 not ok 15 - deconstruct correctly handles cycle in the reference path that spans snarl # got: '1' # expected: '0' not ok 16 - -P -H options return correct number of variants # got: '0' # expected: '2' not ok 17 - -P -H options use correct reference name # got: '0' # expected: '2' ok 18 - -P -H does not find conflict in alt1 in second variant ok 19 - deconstructing vg graph gives same output as xg graph ok 20 - haplotype 1 preserved when deconstructing small test with gbwt ok 21 - haplotype 2 preserved when deconstructing small test with gbwt ok 22 - gbz deconstruction gives same output as gbwt deconstruction not ok 23 - cluster-free deconstruction finds all alt alleles # got: '' # expected: 'GATTTGA,G' not ok 24 - clustered deconstruction finds fewer alt alleles # got: '' # expected: 'G' not ok 25 - clustered deconstruction finds correct allele info # got: '' # expected: '0:0.333:0' 0a1,2 > CATG CAAG,C 1|2 > T A,* 1|2 not ok 26 - nested deconstruction gets correct star-allele for snp inside deletion # got: '1' # expected: '0' not ok 27 - PA=0 correctly set at both sites of neseted deletion # got: '0' # expected: '2' 0a1,2 > CATG CAAG,C 1|2 > T A 1|. not ok 28 - nested deconstruction gets correct allele for snp inside deletion (without -R) # got: '1' # expected: '0' 0a1,2 > A T 0|1 > C CAAG,CATG 1|2 not ok 29 - nested deconstruction gets correct allele for snp inside insert # got: '1' # expected: '0' not ok 30 - PA=0 set for base allele of nested insertion # got: '0' # expected: '1' not ok 31 - PA=1 set for nested allele of nested insertion # got: '0' # expected: '1' 0a1,2 > ##contig= > ##contig= not ok 32 - nested deconstruction gets correct contigs in vcf header for snp inside insert # got: '1' # expected: '0' 0a1,2 > A T,* 0|1 0|2 > C CAAG,CATG 1|2 1|0 not ok 33 - nested deconstruction gets correct star allele for snp ins2.ide ins2.ert # got: '1' # expected: '0' not ok 34 - unnamed test # got: 'AC=1,1;AF=0.5,0.5;AN=2;AT=>1>6,>1>2>3>31>33>34>35>5>6,>1>2>3>31>32>34>35>5>6;NS=1;PA=0;PL=1;PR=1;RC=x;RD=1;RL=1;RS=1;LV=0' # expected: 'INFO tags correct for level-0 site of double-nested SNP' not ok 35 - unnamed test # got: 'AC=1;AF=0.5;AN=2;AT=>2>3>31>33>34>35>5,>2>3>31>32>34>35>5;NS=1;PA=1;PL=8;PR=1;RC=x;RD=1;RL=8;RS=1;LV=1;PS=>1>6' # expected: 'INFO tags correct for level-1 site of double-nested SNP' not ok 36 - unnamed test # got: 'AC=1;AF=0.5;AN=2;AT=>31>33>34,>31>32>34;NS=1;PA=0;PL=5;PR=5;RC=x;RD=1;RL=8;RS=1;LV=2;PS=>2>5' # expected: 'INFO tags correct for level-2 site of double-nested SNP' 0a1,2 > A#1#y0 3 >2>5 A T AC=2;AF=0.5;AN=4;AT=>2>4>5,>2>3>5;NS=2;PA=1;PL=7;PR=1;RC=x;RD=1;RL=7;RS=1;LV=1;PS=>1>6 0|1 0|1 > x 1 >1>6 C CAAGAAG,CATG,CAAG AC=1,2,1;AF=0.25,0.5,0.25;AN=4;AT=>1>6,>1>2>4>5>2>4>5>6,>1>2>3>5>6,>1>2>4>5>6;NS=2;PA=0;PL=1;PR=1;RC=x;RD=1;RL=1;RS=1;LV=0 1|2 3|2 not ok 37 - nested deconstruction handles cycle # got: '1' # expected: '0' Failed 30/37 subtests t/27_vg_genotype.t: line 11: vg: command not found t/27_vg_genotype.t: line 12: vg: command not found t/27_vg_genotype.t: line 13: vg: command not found t/27_vg_genotype.t: line 14: vg: command not found t/27_vg_genotype.t: line 16: vg: command not found t/27_vg_genotype.t: line 19: vg: command not found t/27_vg_genotype.t: line 24: vg: command not found t/27_vg_genotype.t: line 25: vg: command not found t/27_vg_genotype.t: line 28: vg: command not found t/27_vg_genotype.t: line 29: vg: command not found t/27_vg_genotype.t: line 33: vg: command not found t/27_vg_genotype.t: line 34: vg: command not found t/27_vg_genotype.t: line 36: vg: command not found t/27_vg_genotype.t: line 37: vg: command not found t/27_vg_genotype.t: line 39: vg: command not found t/27_vg_genotype.t: line 39: vg: command not found t/27_vg_genotype.t: line 39: vg: command not found t/27_vg_genotype.t: line 39: vg: command not found t/27_vg_genotype.t: line 40: vg: command not found t/27_vg_genotype.t: line 40: vg: command not found t/27_vg_genotype.t: line 40: vg: command not found t/27_vg_genotype.t: line 40: vg: command not found t/27_vg_genotype.t: line 42: vg: command not found t/27_vg_genotype.t: line 42: vg: command not found t/27_vg_genotype.t: line 46: vg: command not found t/27_vg_genotype.t: line 46: vg: command not found t/27_vg_genotype.t: line 46: vg: command not found t/27_vg_genotype.t: line 51: vg: command not found t/27_vg_genotype.t: line 52: vg: command not found t/27_vg_genotype.t: line 54: vg: command not found t/27_vg_genotype.t: line 55: vg: command not found t/27_vg_genotype.t .... 1..5 not ok 1 - vg genotype runs successfully # got: '127' # expected: '0' not ok 2 - vg genotype runs successfully when emitting vcf # got: '127' # expected: '0' ok 3 - called genotypes are correct in a small simulated example not ok 4 - genotype format can be converted to and from JSON # got: '127' # expected: '0' not ok 5 - genotype finds big insert # got: '0' # expected: '1' Failed 4/5 subtests t/28_translate.t: line 10: vg: command not found t/28_translate.t: line 11: vg: command not found t/28_translate.t: line 12: vg: command not found t/28_translate.t: line 12: vg: command not found t/28_translate.t: line 12: vg: command not found t/28_translate.t: line 13: vg: command not found t/28_translate.t: line 14: vg: command not found t/28_translate.t: line 15: vg: command not found t/28_translate.t: line 15: vg: command not found t/28_translate.t: line 15: vg: command not found t/28_translate.t: line 16: vg: command not found t/28_translate.t: line 16: vg: command not found t/28_translate.t: line 16: vg: command not found t/28_translate.t: line 17: vg: command not found t/28_translate.t: line 19: vg: command not found t/28_translate.t: line 19: vg: command not found t/28_translate.t: line 19: vg: command not found t/28_translate.t: line 19: vg: command not found t/28_translate.t: line 19: vg: command not found t/28_translate.t: line 19: vg: command not found t/28_translate.t: line 23: vg: command not found t/28_translate.t: line 24: vg: command not found t/28_translate.t: line 25: vg: command not found t/28_translate.t: line 26: vg: command not found t/28_translate.t: line 27: vg: command not found t/28_translate.t: line 28: vg: command not found t/28_translate.t: line 29: vg: command not found t/28_translate.t: line 30: vg: command not found t/28_translate.t: line 31: vg: command not found t/28_translate.t: line 31: vg: command not found t/28_translate.t: line 31: vg: command not found t/28_translate.t: line 32: vg: command not found t/28_translate.t: line 33: vg: command not found t/28_translate.t: line 34: vg: command not found 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: 'd41d8cd98f00b204e9800998ecf8427e' # expected: '3ce4390abe667b24eb5148e216a2f5ec' Failed 1/2 subtests t/30_vg_chunk.t: line 11: vg: command not found t/30_vg_chunk.t: line 12: vg: command not found t/30_vg_chunk.t: line 13: vg: command not found t/30_vg_chunk.t: line 14: vg: command not found t/30_vg_chunk.t: line 15: vg: command not found t/30_vg_chunk.t: line 16: vg: command not found t/30_vg_chunk.t: line 18: vg: command not found t/30_vg_chunk.t: line 21: vg: command not found t/30_vg_chunk.t: line 21: vg: command not found t/30_vg_chunk.t: line 22: vg: command not found t/30_vg_chunk.t: line 22: vg: command not found t/30_vg_chunk.t: line 25: vg: command not found t/30_vg_chunk.t: line 25: vg: command not found t/30_vg_chunk.t: line 26: vg: command not found t/30_vg_chunk.t: line 26: vg: command not found t/30_vg_chunk.t: line 29: vg: command not found t/30_vg_chunk.t: line 30: vg: command not found t/30_vg_chunk.t: line 30: vg: command not found t/30_vg_chunk.t: line 34: vg: command not found t/30_vg_chunk.t: line 34: vg: command not found t/30_vg_chunk.t: line 34: vg: command not found t/30_vg_chunk.t: line 38: vg: command not found t/30_vg_chunk.t: line 39: vg: command not found ls: cannot access '_chunk_test*.vg': No such file or directory t/30_vg_chunk.t: line 44: vg: command not found t/30_vg_chunk.t: line 46: vg: command not found ls: cannot access '_chunk_test*.vg': No such file or directory ls: cannot access '_chunk_test*.gam': No such file or directory grep: _chunk_test_out.bed: No such file or directory t/30_vg_chunk.t: line 50: vg: command not found t/30_vg_chunk.t: line 50: vg: command not found t/30_vg_chunk.t: line 51: vg: command not found t/30_vg_chunk.t: line 55: vg: command not found ls: cannot access '_chunk_test*.gam': No such file or directory t/30_vg_chunk.t: line 57: vg: command not found t/30_vg_chunk.t: line 60: vg: command not found t/30_vg_chunk.t: line 60: vg: command not found t/30_vg_chunk.t: line 61: vg: command not found t/30_vg_chunk.t: line 61: vg: command not found t/30_vg_chunk.t: line 65: vg: command not found t/30_vg_chunk.t: line 65: vg: command not found t/30_vg_chunk.t: line 68: vg: command not found t/30_vg_chunk.t: line 68: vg: command not found t/30_vg_chunk.t: line 69: vg: command not found t/30_vg_chunk.t: line 69: vg: command not found t/30_vg_chunk.t: line 70: vg: command not found t/30_vg_chunk.t: line 70: vg: command not found t/30_vg_chunk.t: line 71: vg: command not found t/30_vg_chunk.t: line 71: vg: command not found t/30_vg_chunk.t: line 72: vg: command not found t/30_vg_chunk.t: line 72: vg: command not found t/30_vg_chunk.t: line 73: vg: command not found t/30_vg_chunk.t: line 73: vg: command not found t/30_vg_chunk.t: line 75: vg: command not found t/30_vg_chunk.t: line 75: vg: command not found t/30_vg_chunk.t: line 76: vg: command not found t/30_vg_chunk.t: line 76: vg: command not found t/30_vg_chunk.t: line 83: vg: command not found t/30_vg_chunk.t: line 85: vg: command not found t/30_vg_chunk.t: line 88: vg: command not found cat: 'x.chunk/*vg': No such file or directory t/30_vg_chunk.t: line 88: vg: command not found t/30_vg_chunk.t: line 94: vg: command not found t/30_vg_chunk.t: line 95: vg: command not found t/30_vg_chunk.t: line 96: vg: command not found t/30_vg_chunk.t: line 97: vg: command not found t/30_vg_chunk.t: line 98: vg: command not found t/30_vg_chunk.t: line 99: vg: command not found t/30_vg_chunk.t: line 102: vg: command not found t/30_vg_chunk.t: line 103: vg: command not found t/30_vg_chunk.t: line 104: vg: command not found t/30_vg_chunk.t: line 105: vg: command not found t/30_vg_chunk.t: line 105: vg: command not found t/30_vg_chunk.t: line 106: vg: command not found t/30_vg_chunk.t: line 106: vg: command not found t/30_vg_chunk.t: line 109: vg: command not found t/30_vg_chunk.t: line 109: vg: command not found t/30_vg_chunk.t: line 110: vg: command not found t/30_vg_chunk.t: line 110: vg: command not found t/30_vg_chunk.t: line 111: vg: command not found t/30_vg_chunk.t: line 112: vg: command not found t/30_vg_chunk.t: line 113: vg: command not found t/30_vg_chunk.t: line 113: vg: command not found t/30_vg_chunk.t: line 114: vg: command not found t/30_vg_chunk.t: line 114: vg: command not found t/30_vg_chunk.t: line 115: vg: command not found t/30_vg_chunk.t: line 116: vg: command not found t/30_vg_chunk.t: line 119: vg: command not found t/30_vg_chunk.t: line 120: vg: command not found t/30_vg_chunk.t: line 121: vg: command not found t/30_vg_chunk.t ....... 1..32 not ok 1 - unnamed test # got: '210' # expected: 'vg chunk with no options preserves nodes' not ok 2 - unnamed test # got: '291' # expected: 'vg chunk with no options preserves edges' not ok 3 - chunk has path going through node 9 # got: '0' # expected: '1' not ok 4 - chunk can be found from GBZ # got: '0' # expected: '1' not ok 5 - unnamed test # got: '6789' # expected: 'snarl chunk works on simple example' not ok 6 - chunk has path going through node 9 # got: '0' # expected: '1' not ok 7 - -s produces correct number of chunks # got: '0' # expected: '6' not ok 8 - gam chunker produces correct number of graphs # got: '0' # expected: '2' not ok 9 - gam chunker produces correct number of gams # got: '0' # expected: '2' not ok 10 - gam chunker produces bed with correct number of chunks # got: '0' # expected: '2' ok 11 - gam chunker emits each matching read at most once not ok 12 - chunk contains the expected number of alignments # got: '0' # expected: '225' not ok 13 - simple gam chunker produces correct number of gams # got: '0' # expected: '10' not ok 14 - simple chunk contains the expected number of alignments # got: '0' # expected: '100' not ok 15 - id chunker produces correct chunk size # got: '0' # expected: '3' not ok 16 - id chunker produces correct single chunk # got: '0' # expected: '1' not ok 17 - id chunker traces correct chunk size without haplotypes # got: '0' # expected: '5' not ok 18 - id chunker traces correct chunk size # got: '0' # expected: '5' ok 19 - chunker extracts no threads from an empty gPBWT not ok 20 - chunker extracts 2 local threads from a gBWT with 2 locally distinct threads in it # got: '0' # expected: '2' not ok 21 - chunker can extract a partial haplotype from a GBWT # got: '' # expected: '3' not ok 22 - chunker can extract a partial haplotype from a GBZ # got: '' # expected: '3' ok 23 - chunker doesn't see haplotypes in the GBZ if asked not to ok 24 - trace consistent on path coordinates ok 25 - n-chunking works and chunks over the full graph ok 26 - path-based components finds subgraphs ok 27 - x gam chunk has correct number of reads ok 28 - y gam chunk has correct number of reads ok 29 - x gam chunk has correct number of reads with -p path ok 30 - y gam chunk has correct number of reads with -p path ok 31 - path-based component contains correct path length ok 32 - components finds subgraphs Failed 20/32 subtests t/31_vg_add.t: line 10: vg: command not found t/31_vg_add.t: line 11: vg: command not found t/31_vg_add.t: line 14: vg: command not found t/31_vg_add.t: line 20: vg: command not found t/31_vg_add.t: line 21: vg: command not found t/31_vg_add.t: line 27: vg: command not found t/31_vg_add.t: line 28: vg: command not found t/31_vg_add.t: line 29: vg: command not found t/31_vg_add.t: line 31: vg: command not found t/31_vg_add.t: line 31: vg: command not found t/31_vg_add.t: line 33: vg: command not found t/31_vg_add.t: line 34: vg: command not found t/31_vg_add.t: line 37: vg: command not found t/31_vg_add.t: line 39: vg: command not found t/31_vg_add.t: line 40: vg: command not found t/31_vg_add.t: line 43: vg: command not found t/31_vg_add.t: line 45: vg: command not found t/31_vg_add.t: line 45: vg: command not found t/31_vg_add.t: line 45: vg: command not found t/31_vg_add.t: line 45: vg: command not found t/31_vg_add.t: line 47: vg: command not found t/31_vg_add.t: line 47: vg: command not found t/31_vg_add.t: line 47: vg: command not found t/31_vg_add.t: line 47: vg: command not found t/31_vg_add.t: line 49: vg: command not found t/31_vg_add.t: line 49: vg: command not found t/31_vg_add.t: line 49: vg: command not found t/31_vg_add.t: line 49: vg: command not found t/31_vg_add.t ......... 1..12 not ok 1 - vg add can create a graph # got: '127' # expected: '0' not ok 2 - vg add can create a graph with contig renames # got: '127' # expected: '0' ok 3 - vg add produces the same graph from VCFs with different contig names not ok 4 - vg add can create a graph from a PackedGraph # got: '127' # expected: '0' 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 not ok 7 - adding variants adds only the alt bases near large N gaps # got: '' # expected: '73315' not ok 8 - vg add can create a slightly larger graph # got: '127' # expected: '0' 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 8/12 subtests t/32_vg_snarls.t: line 10: vg: command not found t/32_vg_snarls.t: line 11: vg: command not found t/32_vg_snarls.t: line 12: vg: command not found t/32_vg_snarls.t: line 13: vg: command not found t/32_vg_snarls.t: line 14: vg: command not found t/32_vg_snarls.t: line 18: vg: command not found t/32_vg_snarls.t: line 19: vg: command not found t/32_vg_snarls.t: line 19: vg: command not found t/32_vg_snarls.t: line 20: vg: command not found t/32_vg_snarls.t: line 25: vg: command not found t/32_vg_snarls.t: line 26: vg: command not found t/32_vg_snarls.t: line 27: vg: command not found t/32_vg_snarls.t: line 28: vg: command not found t/32_vg_snarls.t: line 29: vg: command not found t/32_vg_snarls.t: line 36: vg: command not found t/32_vg_snarls.t: line 37: vg: command not found t/32_vg_snarls.t: line 38: vg: command not found t/32_vg_snarls.t: line 39: vg: command not found t/32_vg_snarls.t: line 40: vg: command not found t/32_vg_snarls.t: line 47: vg: command not found t/32_vg_snarls.t: line 48: vg: command not found t/32_vg_snarls.t: line 49: vg: command not found t/32_vg_snarls.t: line 50: vg: command not found t/32_vg_snarls.t: line 51: vg: command not found t/32_vg_snarls.t: line 58: vg: command not found t/32_vg_snarls.t: line 59: vg: command not found t/32_vg_snarls.t: line 60: vg: command not found t/32_vg_snarls.t: line 61: vg: command not found t/32_vg_snarls.t: line 62: vg: command not found t/32_vg_snarls.t: line 63: vg: command not found t/32_vg_snarls.t: line 63: vg: command not found t/32_vg_snarls.t: line 64: vg: command not found t/32_vg_snarls.t: line 64: vg: command not found t/32_vg_snarls.t: line 64: vg: command not found t/32_vg_snarls.t: line 68: vg: command not found t/32_vg_snarls.t: line 69: vg: command not found t/32_vg_snarls.t: line 71: vg: command not found t/32_vg_snarls.t: line 76: vg: command not found t/32_vg_snarls.t: line 77: vg: command not found t/32_vg_snarls.t: line 81: vg: command not found t/32_vg_snarls.t: line 88: vg: command not found t/32_vg_snarls.t: line 88: vg: command not found t/32_vg_snarls.t: line 93: vg: command not found t/32_vg_snarls.t: line 94: vg: command not found t/32_vg_snarls.t: line 95: vg: command not found t/32_vg_snarls.t: line 96: vg: command not found t/32_vg_snarls.t: line 99: vg: command not found t/32_vg_snarls.t: line 100: vg: command not found t/32_vg_snarls.t: line 101: vg: command not found t/32_vg_snarls.t ...... 1..19 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 - unnamed test # got: '1,3,7,' # expected: 'vg snarls made snarls in the right order' not ok 4 - vg snarls on xg made right number of protobuf Snarls # got: '0' # expected: '3' not ok 5 - vg snarls on xg made right number of protobuf SnarlTraversals # got: '0' # expected: '6' ok 6 - vcf traversals are the same as exhaustive traversals for tiny graph ok 7 - vcf traversals are the same as exhaustive traversals for inversion ok 8 - vcf traversals are the same as exhaustive traversals for ins_and_del graph not ok 9 - correct number of snarls when parallelizing on compoents # got: '0' # expected: '35' ok 10 - same number of snarls when parallelizing on components not ok 11 - GBZ graphs can be used for finding snarls # got: '127' # expected: '0' not ok 12 - correct number of snarls in the GFA W-line example # got: '0' # expected: '5' not ok 13 - vg snarls made the right snarls when dealing with nested chains # got: '1' # expected: '15' not ok 14 - vg snarls made snarls in the right order when dealing with nested chains # got: '1' # expected: '0' not ok 15 - Correct snarls are found in GFA space # got: '' # expected: '["cats",null,"goldfish",null] # ["goldfish",null,"sparrows",null] # ["pigs",true,"squirrels",null] # ["squirrels",null,"rabbits",true]' not ok 16 - In node ID space traversal visits 7 nodes # got: '0' # expected: '7' not ok 17 - In node ID space traversal visits 4 trivial snarls # got: '0' # expected: '4' not ok 18 - In segment name space traversal visits 3 segments # got: '0' # expected: '3' ok 19 - In segment name space traversal visits 0 trivial snarls Failed 14/19 subtests t/33_vg_mpmap.t: line 13: vg: command not found t/33_vg_mpmap.t: line 14: vg: command not found t/33_vg_mpmap.t: line 19: vg: command not found t/33_vg_mpmap.t: line 19: vg: command not found t/33_vg_mpmap.t: line 20: vg: command not found t/33_vg_mpmap.t: line 20: vg: command not found t/33_vg_mpmap.t: line 21: vg: command not found t/33_vg_mpmap.t: line 21: vg: command not found t/33_vg_mpmap.t: line 24: vg: command not found t/33_vg_mpmap.t: line 24: vg: command not found t/33_vg_mpmap.t: line 25: vg: command not found t/33_vg_mpmap.t: line 26: vg: command not found t/33_vg_mpmap.t: line 27: vg: command not found t/33_vg_mpmap.t: line 36: vg: command not found t/33_vg_mpmap.t: line 38: vg: command not found t/33_vg_mpmap.t: line 38: vg: command not found t/33_vg_mpmap.t: line 39: vg: command not found t/33_vg_mpmap.t: line 39: vg: command not found t/33_vg_mpmap.t: line 40: vg: command not found t/33_vg_mpmap.t: line 40: vg: command not found t/33_vg_mpmap.t: line 41: vg: command not found t/33_vg_mpmap.t: line 41: vg: command not found t/33_vg_mpmap.t: line 47: vg: command not found t/33_vg_mpmap.t: line 49: vg: command not found t/33_vg_mpmap.t: line 49: vg: command not found t/33_vg_mpmap.t: line 50: vg: command not found t/33_vg_mpmap.t: line 50: vg: command not found t/33_vg_mpmap.t: line 51: vg: command not found t/33_vg_mpmap.t: line 51: vg: command not found t/33_vg_mpmap.t: line 64: vg: command not found t/33_vg_mpmap.t: line 66: vg: command not found t/33_vg_mpmap.t: line 67: vg: command not found t/33_vg_mpmap.t: line 73: vg: command not found t/33_vg_mpmap.t: line 74: vg: command not found t/33_vg_mpmap.t: line 89: vg: command not found t/33_vg_mpmap.t: line 89: vg: command not found rm: cannot remove 't.xg': No such file or directory rm: cannot remove 't.gcsa': No such file or directory rm: cannot remove 't.gcsa.lcp': No such file or directory t/33_vg_mpmap.t: line 95: vg: command not found t/33_vg_mpmap.t: line 96: vg: command not found t/33_vg_mpmap.t: line 97: vg: command not found t/33_vg_mpmap.t: line 98: vg: command not found t/33_vg_mpmap.t: line 105: vg: command not found t/33_vg_mpmap.t: line 105: vg: command not found t/33_vg_mpmap.t: line 105: vg: command not found t/33_vg_mpmap.t: line 117: vg: command not found t/33_vg_mpmap.t: line 117: vg: command not found t/33_vg_mpmap.t: line 128: vg: command not found t/33_vg_mpmap.t: line 128: vg: command not found t/33_vg_mpmap.t: line 130: vg: command not found rm: cannot remove 's.xg': No such file or directory rm: cannot remove 's.gcsa': No such file or directory rm: cannot remove 's.gcsa.lcp': No such file or directory rm: cannot remove 's.dist': No such file or directory t/33_vg_mpmap.t: line 135: vg: command not found t/33_vg_mpmap.t: line 136: vg: command not found t/33_vg_mpmap.t: line 138: vg: command not found t/33_vg_mpmap.t: line 139: vg: command not found t/33_vg_mpmap.t: line 140: vg: command not found t/33_vg_mpmap.t: line 141: vg: command not found t/33_vg_mpmap.t: line 143: vg: command not found t/33_vg_mpmap.t: line 152: vg: command not found rm: cannot remove 'xy.xg': No such file or directory rm: cannot remove 'xy.gcsa': No such file or directory t/33_vg_mpmap.t ....... 1..21 not ok 1 - MAPQ is 50% without haplotype info # got: '' # expected: '3' not ok 2 - haplotype match can disambiguate # got: '' # expected: '4' not ok 3 - MAPQs are computed for all multimappings # got: '' # expected: '2' not ok 4 - MAPQ is 50% when paired without haplotype info # got: '' # expected: '3' not ok 5 - haplotype match can disambiguate paired # got: '' # expected: '4' not ok 6 - use of haplotype-aware mapping is recorded # got: '' # expected: 'true' not ok 7 - Haplotype-oblivious mapping places read on the wrong contig # got: '' # expected: '50' not ok 8 - Haplotype-oblivious mapping places read with MAPQ of 50% # got: '' # expected: '3' not ok 9 - Haplotype-aware mapping places read on the right contig # got: '' # expected: '1' not ok 10 - Haplotype-aware mapping places read with MAPQ > 50% # got: '' # expected: '6' not ok 11 - paired read alignments forced to be consistent have lower score than unrestricted alignments # got: '0' # expected: '1' not ok 12 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments # got: '0' # expected: '1' not ok 13 - paired read alignments forced to be near each other are closer together in node id space than those forced to be far apart # got: '0' # expected: '1' ok 14 - small batches are still all paired in the output not ok 15 - multipath mapping works in scenarios that trigger branch point trimming # got: '0' # expected: '3' not ok 16 - spliced alignments can be found when aligning RNA # got: '' # expected: '105' not ok 17 - paired mapping can identify a splice junction on read 1 # got: '0' # expected: '1' not ok 18 - paired mapping can identify a splice junction on read 2 # got: '0' # expected: '1' not ok 19 - HTS output contains group mapq annotation # got: '0' # expected: '2' not ok 20 - paired reads are evenly split between equivalent mappings # got: '0' # expected: '1' not ok 21 - unpaired reads are evenly split between equivalent mappings # got: '0' # expected: '1' Dubious, test returned 1 (wstat 256, 0x100) Failed 20/21 subtests t/34_vg_pack.t: line 10: vg: command not found t/34_vg_pack.t: line 11: vg: command not found t/34_vg_pack.t: line 11: vg: command not found t/34_vg_pack.t: line 12: vg: command not found t/34_vg_pack.t: line 13: vg: command not found t/34_vg_pack.t: line 14: vg: command not found t/34_vg_pack.t: line 15: vg: command not found t/34_vg_pack.t: line 16: vg: command not found t/34_vg_pack.t: line 17: vg: command not found t/34_vg_pack.t: line 20: vg: command not found t/34_vg_pack.t: line 22: vg: command not found t/34_vg_pack.t: line 25: vg: command not found t/34_vg_pack.t: line 27: vg: command not found (standard_in) 1: syntax error t/34_vg_pack.t: line 27: vg: command not found (standard_in) 1: syntax error t/34_vg_pack.t: line 29: vg: command not found (standard_in) 1: syntax error t/34_vg_pack.t: line 29: vg: command not found (standard_in) 1: syntax error t/34_vg_pack.t: line 31: vg: command not found t/34_vg_pack.t: line 32: vg: command not found t/34_vg_pack.t: line 33: vg: command not found t/34_vg_pack.t: line 36: vg: command not found t/34_vg_pack.t: line 37: vg: command not found t/34_vg_pack.t: line 40: vg: command not found t/34_vg_pack.t: line 41: vg: command not found t/34_vg_pack.t: line 44: vg: command not found t/34_vg_pack.t: line 45: vg: command not found t/34_vg_pack.t: line 46: vg: command not found t/34_vg_pack.t: line 47: vg: command not found t/34_vg_pack.t: line 48: vg: command not found t/34_vg_pack.t: line 52: vg: command not found t/34_vg_pack.t: line 53: vg: command not found t/34_vg_pack.t: line 54: vg: command not found t/34_vg_pack.t: line 55: vg: command not found t/34_vg_pack.t: line 56: vg: command not found t/34_vg_pack.t: line 62: vg: command not found t/34_vg_pack.t: line 63: vg: command not found t/34_vg_pack.t: line 66: vg: command not found t/34_vg_pack.t: line 68: vg: command not found t/34_vg_pack.t: line 73: vg: command not found t/34_vg_pack.t: line 74: vg: command not found t/34_vg_pack.t: line 75: vg: command not found t/34_vg_pack.t: line 76: vg: command not found t/34_vg_pack.t: line 77: vg: command not found t/34_vg_pack.t: line 78: vg: command not found t/34_vg_pack.t: line 79: vg: command not found t/34_vg_pack.t: line 83: vg: command not found t/34_vg_pack.t: line 84: vg: command not found t/34_vg_pack.t: line 88: vg: command not found t/34_vg_pack.t: line 92: vg: command not found t/34_vg_pack.t: line 96: vg: command not found t/34_vg_pack.t: line 96: vg: command not found t/34_vg_pack.t: line 97: vg: command not found t/34_vg_pack.t: line 101: vg: command not found t/34_vg_pack.t: line 107: vg: command not found t/34_vg_pack.t: line 108: vg: command not found t/34_vg_pack.t: line 110: vg: command not found t/34_vg_pack.t: line 110: vg: command not found t/34_vg_pack.t: line 110: vg: command not found t/34_vg_pack.t: line 112: vg: command not found t/34_vg_pack.t: line 112: vg: command not found t/34_vg_pack.t: line 112: vg: command not found t/34_vg_pack.t: line 114: vg: command not found t/34_vg_pack.t: line 114: vg: command not found t/34_vg_pack.t: line 114: vg: command not found t/34_vg_pack.t: line 115: vg: command not found t/34_vg_pack.t: line 116: vg: command not found t/34_vg_pack.t: line 120: vg: command not found t/34_vg_pack.t: line 121: vg: command not found t/34_vg_pack.t: line 122: vg: command not found t/34_vg_pack.t: line 123: vg: command not found t/34_vg_pack.t: line 126: vg: command not found t/34_vg_pack.t: line 128: vg: command not found t/34_vg_pack.t: line 133: vg: command not found t/34_vg_pack.t: line 136: vg: command not found t/34_vg_pack.t: line 138: vg: command not found t/34_vg_pack.t ........ 1..20 not ok 1 - allele observation packing detects 2 SNPs # got: '0' # expected: '2' not ok 2 - pileup packs agree with graph coverage # got: 'f9108e41700ebf9a7be4b41322033704' # expected: 'd41d8cd98f00b204e9800998ecf8427e' not ok 3 - unnamed test # got: 'graph coverages are merged from multiple .cx indexes' # expected: '' not ok 4 - unnamed test # got: 'edit records are merged from multiple .cx indexes' # expected: '' 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 not ok 10 - unnamed test # got: '88' # expected: 'pack computes the same total edge coverage as pileup' not ok 11 - unnamed test # got: 'pack stores the correct edge pileup to disk' # expected: '' 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 - unnamed test # got: '20-15-10-10-0-0-0-0-60-60-' # expected: 'average node qualities are correct' 1,20d0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 not ok 19 - pack -s 10 sets fist and last 10bp of coverage to 0 like expected # got: '1' # expected: '0' 1,18d0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 < 0 not ok 20 - pack -s 9 sets fist and last 9bp of coverage to 0 like expected # got: '1' # expected: '0' Failed 9/20 subtests t/36_vg_annotate.t: line 10: vg: command not found t/36_vg_annotate.t: line 12: vg: command not found t/36_vg_annotate.t: line 13: vg: command not found t/36_vg_annotate.t: line 14: vg: command not found t/36_vg_annotate.t: line 16: vg: command not found t/36_vg_annotate.t: line 18: vg: command not found t/36_vg_annotate.t: line 19: vg: command not found t/36_vg_annotate.t: line 20: vg: command not found t/36_vg_annotate.t: line 20: vg: command not found t/36_vg_annotate.t: line 21: vg: command not found t/36_vg_annotate.t: line 22: vg: command not found t/36_vg_annotate.t: line 23: vg: command not found t/36_vg_annotate.t: line 27: vg: command not found t/36_vg_annotate.t: line 28: vg: command not found t/36_vg_annotate.t: line 30: vg: command not found t/36_vg_annotate.t: line 32: vg: command not found t/36_vg_annotate.t: line 32: vg: command not found t/36_vg_annotate.t: line 33: vg: command not found t/36_vg_annotate.t: line 33: vg: command not found t/36_vg_annotate.t: line 37: vg: command not found t/36_vg_annotate.t: line 38: vg: command not found t/36_vg_annotate.t: line 39: vg: command not found t/36_vg_annotate.t: line 41: vg: command not found t/36_vg_annotate.t .... 1..9 not ok 1 - we can detect when reads contain non-reference variation # got: '0' # expected: '10' not ok 2 - vg annotate finds the right number of reads overlapping a feature # got: '0' # expected: '3' ok 3 - all reads overlapping a feature fall on its node ok 4 - vg annotate finds no reads touching both of two distant features not ok 5 - vg annotate shows reads having to go through one feature to get to another at the end # got: '0' # expected: '2' not ok 6 - vg annotate shows all reads overlapping a whole-reference-covering feature # got: '0' # expected: '30' not ok 7 - annotating with earliest path position produces one position # got: '0' # expected: '1' not ok 8 - annotating with multiple path positions produces multiple positions # got: '0' # expected: '13' 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 7/9 subtests t/37_vg_gbwt.t: line 14: vg: command not found t/37_vg_gbwt.t: line 16: vg: command not found t/37_vg_gbwt.t: line 17: vg: command not found t/37_vg_gbwt.t: line 18: vg: command not found t/37_vg_gbwt.t: line 22: vg: command not found t/37_vg_gbwt.t: line 24: vg: command not found cmp: x.gbwt: No such file or directory t/37_vg_gbwt.t: line 28: vg: command not found cmp: x.gbwt: No such file or directory t/37_vg_gbwt.t: line 36: vg: command not found t/37_vg_gbwt.t: line 37: vg: command not found t/37_vg_gbwt.t: line 38: vg: command not found t/37_vg_gbwt.t: line 39: vg: command not found t/37_vg_gbwt.t: line 40: vg: command not found t/37_vg_gbwt.t: line 41: vg: command not found t/37_vg_gbwt.t: line 42: vg: command not found t/37_vg_gbwt.t: line 49: vg: command not found t/37_vg_gbwt.t: line 51: vg: command not found cmp: x.ref.gbwt: No such file or directory t/37_vg_gbwt.t: line 55: vg: command not found t/37_vg_gbwt.t: line 61: vg: command not found t/37_vg_gbwt.t: line 62: vg: command not found t/37_vg_gbwt.t: line 63: vg: command not found t/37_vg_gbwt.t: line 65: vg: command not found cmp: x.alts.gaf.gbwt: No such file or directory t/37_vg_gbwt.t: line 69: vg: command not found cmp: x.alts.gaf.gbwt: No such file or directory t/37_vg_gbwt.t: line 79: vg: command not found cmp: x.part.gbwt: No such file or directory t/37_vg_gbwt.t: line 92: vg: command not found t/37_vg_gbwt.t: line 93: vg: command not found t/37_vg_gbwt.t: line 94: vg: command not found t/37_vg_gbwt.t: line 96: vg: command not found cmp: xy.merge.gbwt: No such file or directory t/37_vg_gbwt.t: line 100: vg: command not found cmp: xy.merge.gbwt: No such file or directory t/37_vg_gbwt.t: line 104: vg: command not found cmp: xy.direct.gbwt: No such file or directory t/37_vg_gbwt.t: line 108: vg: command not found cmp: xy.direct.gbwt: No such file or directory t/37_vg_gbwt.t: line 114: vg: command not found t/37_vg_gbwt.t: line 118: vg: command not found t/37_vg_gbwt.t: line 119: vg: command not found t/37_vg_gbwt.t: line 120: vg: command not found t/37_vg_gbwt.t: line 121: vg: command not found t/37_vg_gbwt.t: line 128: vg: command not found t/37_vg_gbwt.t: line 130: vg: command not found cmp: xy.contigs.gbwt: No such file or directory t/37_vg_gbwt.t: line 134: vg: command not found t/37_vg_gbwt.t: line 135: vg: command not found t/37_vg_gbwt.t: line 136: vg: command not found t/37_vg_gbwt.t: line 137: vg: command not found t/37_vg_gbwt.t: line 144: vg: command not found t/37_vg_gbwt.t: line 151: vg: command not found t/37_vg_gbwt.t: line 155: vg: command not found cmp: x.gbwt: No such file or directory cmp: x.gbwt: No such file or directory t/37_vg_gbwt.t: line 167: vg: command not found cmp: x.gbwt: No such file or directory t/37_vg_gbwt.t: line 173: vg: command not found cmp: x.gbwt: No such file or directory t/37_vg_gbwt.t: line 179: vg: command not found cmp: x.gbwt: No such file or directory cmp: x.gbwt: No such file or directory t/37_vg_gbwt.t: line 194: vg: command not found t/37_vg_gbwt.t: line 195: vg: command not found t/37_vg_gbwt.t: line 196: vg: command not found t/37_vg_gbwt.t: line 197: vg: command not found t/37_vg_gbwt.t: line 200: vg: command not found t/37_vg_gbwt.t: line 202: vg: command not found t/37_vg_gbwt.t: line 208: vg: command not found t/37_vg_gbwt.t: line 209: vg: command not found t/37_vg_gbwt.t: line 210: vg: command not found t/37_vg_gbwt.t: line 213: vg: command not found t/37_vg_gbwt.t: line 215: vg: command not found t/37_vg_gbwt.t: line 216: vg: command not found t/37_vg_gbwt.t: line 222: vg: command not found t/37_vg_gbwt.t: line 223: vg: command not found cat: x.extract: No such file or directory t/37_vg_gbwt.t: line 231: vg: command not found md5sum: x.gg: No such file or directory t/37_vg_gbwt.t: line 236: vg: command not found md5sum: x.gbz: No such file or directory t/37_vg_gbwt.t: line 241: vg: command not found cmp: x.gbz: No such file or directory t/37_vg_gbwt.t: line 247: vg: command not found cmp: x.gbz: No such file or directory t/37_vg_gbwt.t: line 253: vg: command not found cmp: x.gbwt: No such file or directory t/37_vg_gbwt.t: line 259: vg: command not found cmp: x.gbwt: No such file or directory cmp: x.gg: No such file or directory t/37_vg_gbwt.t: line 271: vg: command not found md5sum: xy.cover.gg: No such file or directory t/37_vg_gbwt.t: line 274: vg: command not found t/37_vg_gbwt.t: line 275: vg: command not found t/37_vg_gbwt.t: line 276: vg: command not found t/37_vg_gbwt.t: line 277: vg: command not found t/37_vg_gbwt.t: line 282: vg: command not found md5sum: xy.cover.gg: No such file or directory t/37_vg_gbwt.t: line 285: vg: command not found t/37_vg_gbwt.t: line 286: vg: command not found t/37_vg_gbwt.t: line 287: vg: command not found t/37_vg_gbwt.t: line 288: vg: command not found t/37_vg_gbwt.t: line 293: vg: command not found md5sum: xy.local.gg: No such file or directory t/37_vg_gbwt.t: line 296: vg: command not found t/37_vg_gbwt.t: line 297: vg: command not found t/37_vg_gbwt.t: line 298: vg: command not found t/37_vg_gbwt.t: line 299: vg: command not found t/37_vg_gbwt.t: line 302: vg: command not found md5sum: xy.local.gbz: No such file or directory t/37_vg_gbwt.t: line 307: vg: command not found md5sum: xy.local.gbz: No such file or directory t/37_vg_gbwt.t: line 314: vg: command not found md5sum: xy.local.gg: No such file or directory t/37_vg_gbwt.t: line 317: vg: command not found t/37_vg_gbwt.t: line 318: vg: command not found t/37_vg_gbwt.t: line 319: vg: command not found t/37_vg_gbwt.t: line 320: vg: command not found t/37_vg_gbwt.t: line 325: vg: command not found t/37_vg_gbwt.t: line 326: vg: command not found t/37_vg_gbwt.t: line 328: vg: command not found t/37_vg_gbwt.t: line 329: vg: command not found t/37_vg_gbwt.t: line 330: vg: command not found t/37_vg_gbwt.t: line 331: vg: command not found t/37_vg_gbwt.t: line 332: vg: command not found t/37_vg_gbwt.t: line 338: vg: command not found t/37_vg_gbwt.t: line 339: vg: command not found md5sum: augmented.gg: No such file or directory t/37_vg_gbwt.t: line 342: vg: command not found t/37_vg_gbwt.t: line 343: vg: command not found t/37_vg_gbwt.t: line 344: vg: command not found t/37_vg_gbwt.t: line 345: vg: command not found t/37_vg_gbwt.t: line 355: vg: command not found md5sum: gfa.gbwt: No such file or directory t/37_vg_gbwt.t: line 358: vg: command not found t/37_vg_gbwt.t: line 359: vg: command not found t/37_vg_gbwt.t: line 360: vg: command not found t/37_vg_gbwt.t: line 361: vg: command not found t/37_vg_gbwt.t: line 364: vg: command not found cmp: gfa.gbwt: No such file or directory md5sum: gfa2.gg: No such file or directory t/37_vg_gbwt.t: line 369: gfa2.trans: No such file or directory t/37_vg_gbwt.t: line 372: vg: command not found md5sum: gfa2.gbz: No such file or directory t/37_vg_gbwt.t: line 377: vg: command not found t/37_vg_gbwt.t: line 379: vg: command not found t/37_vg_gbwt.t: line 380: vg: command not found t/37_vg_gbwt.t: line 381: vg: command not found t/37_vg_gbwt.t: line 382: vg: command not found t/37_vg_gbwt.t: line 383: chopping.trans: No such file or directory t/37_vg_gbwt.t: line 386: vg: command not found t/37_vg_gbwt.t: line 387: vg: command not found t/37_vg_gbwt.t: line 389: from_gbz.trans: No such file or directory t/37_vg_gbwt.t: line 392: vg: command not found t/37_vg_gbwt.t: line 394: vg: command not found t/37_vg_gbwt.t: line 395: vg: command not found t/37_vg_gbwt.t: line 396: vg: command not found t/37_vg_gbwt.t: line 397: vg: command not found t/37_vg_gbwt.t: line 398: ref_paths.trans: No such file or directory t/37_vg_gbwt.t: line 406: vg: command not found t/37_vg_gbwt.t: line 408: vg: command not found t/37_vg_gbwt.t: line 411: vg: command not found t/37_vg_gbwt.t: line 413: vg: command not found t/37_vg_gbwt.t: line 414: vg: command not found t/37_vg_gbwt.t: line 417: vg: command not found t/37_vg_gbwt.t: line 419: vg: command not found t/37_vg_gbwt.t: line 424: vg: command not found t/37_vg_gbwt.t: line 425: vg: command not found t/37_vg_gbwt.t ........ 1..159 not ok 1 - chromosome X GBWT with vg gbwt # got: '127' # expected: '0' not ok 2 - chromosome X GBWT with vg index # got: '127' # expected: '0' not ok 3 - identical construction results with vg gbwt and vg index # got: '2' # expected: '0' not ok 4 - chromosome X VCF parse # got: '127' # expected: '0' not ok 5 - chromosome X GBWT from VCF parse # got: '1' # expected: '0' not ok 6 - identical construction results with vg gbwt and from VCF parse # got: '2' # expected: '0' not ok 7 - unnamed test # got: '2' # expected: 'chromosome X: 2 threads' not ok 8 - unnamed test # got: '1' # expected: 'chromosome X: 1 contig' not ok 9 - unnamed test # got: '2' # expected: 'chromosome X: 2 haplotypes' not ok 10 - unnamed test # got: '1' # expected: 'chromosome X: 1 sample' not ok 11 - chromosome X: 2 thread names # got: '0' # expected: '2' not ok 12 - chromosome X: 1 contig name # got: '0' # expected: '1' not ok 13 - chromosome X: 1 sample name # got: '0' # expected: '1' not ok 14 - chromosome X reference GBWT with vg gbwt # got: '127' # expected: '0' not ok 15 - chromosome X reference GBWT with vg index # got: '127' # expected: '0' not ok 16 - identical construction results with vg gbwt and vg index # got: '2' # expected: '0' not ok 17 - unnamed test # got: '1' # expected: 'chromosome X reference: 1 thread' not ok 18 - chromosome X GAF with vg gbwt # got: '127' # expected: '0' not ok 19 - chromosome X GAF with vg index # got: '127' # expected: '0' not ok 20 - identical construction results with vg gbwt and vg index # got: '2' # expected: '0' not ok 21 - chromosome X GAM with vg gbwt # got: '127' # expected: '0' not ok 22 - identical construction results from GAF and GAM # got: '2' # expected: '0' not ok 23 - chromosome X subgraph GBWT with vg gbwt # got: '127' # expected: '0' not ok 24 - no warnings about missing variants # got: '47' # expected: '0' not ok 25 - chromosome X subgraph GBWT with vg index # got: '127' # expected: '0' not ok 26 - identical construction results with vg gbwt and vg index # got: '2' # expected: '0' not ok 27 - insertion merging with multiple chromosomes # got: '127' # expected: '0' not ok 28 - fast merging with multiple chromosomes # got: '127' # expected: '0' not ok 29 - identical merging results with the insertion and fast algorithms # got: '2' # expected: '0' not ok 30 - parallel merging with multiple chromosomes # got: '127' # expected: '0' not ok 31 - identical merging results with the insertion and parallel algorithms # got: '2' # expected: '0' not ok 32 - direct construction with multiple chromosomes and a single VCF # got: '127' # expected: '0' not ok 33 - identical results with direct construction and merging # got: '2' # expected: '0' not ok 34 - direct construction with multiple chromosomes and multiple VCFs # got: '127' # expected: '0' not ok 35 - identical construction results with a single VCF and multiple VCFs # got: '2' # expected: '0' not ok 36 - construction preset: 1000gp # got: '127' # expected: '0' not ok 37 - unnamed test # got: '4' # expected: 'multiple chromosomes: 4 threads' not ok 38 - unnamed test # got: '2' # expected: 'multiple chromosomes: 2 contigs' not ok 39 - unnamed test # got: '2' # expected: 'multiple chromosomes: 2 haplotypes' not ok 40 - unnamed test # got: '1' # expected: 'multiple chromosomes: 1 sample' not ok 41 - paths as contigs with vg gbwt # got: '127' # expected: '0' not ok 42 - paths as contigs with vg index # got: '127' # expected: '0' not ok 43 - identical construction results with vg gbwt and vg index # got: '2' # expected: '0' not ok 44 - unnamed test # got: '2' # expected: 'paths as contigs: 2 threads' not ok 45 - unnamed test # got: '2' # expected: 'paths as contigs: 2 contigs' not ok 46 - unnamed test # got: '1' # expected: 'paths as contigs: 1 haplotype' not ok 47 - unnamed test # got: '1' # expected: 'paths as contigs: 1 sample' not ok 48 - r-index construction # got: '127' # expected: '0' not ok 49 - normal merging: non-empty + empty # got: '127' # expected: '0' not ok 50 - the index remains unchanged # got: '2' # expected: '0' not ok 51 - normal merging: empty + non-empty # got: '127' # expected: '0' not ok 52 - the index remains unchanged # got: '2' # expected: '0' not ok 53 - fast merging: non-empty + empty # got: '127' # expected: '0' not ok 54 - the index remains unchanged # got: '2' # expected: '0' not ok 55 - fast merging: empty + non-empty # got: '127' # expected: '0' not ok 56 - the index remains unchanged # got: '2' # expected: '0' not ok 57 - parallel merging: non-empty + empty # got: '127' # expected: '0' not ok 58 - the index remains unchanged # got: '2' # expected: '0' not ok 59 - parallel merging: empty + non-empty # got: '127' # expected: '0' not ok 60 - the index remains unchanged # got: '2' # expected: '0' not ok 61 - unnamed test # got: '6' # expected: 'haplotypes and paths: 6 threads' not ok 62 - samples can be removed from a GBWT index # got: '127' # expected: '0' not ok 63 - unnamed test # got: '4' # expected: 'haplotypes only: 4 threads' not ok 64 - unnamed test # got: '12' # expected: 'all samples: 12 threads' not ok 65 - unnamed test # got: '6' # expected: 'all samples: 6 haplotypes' not ok 66 - multiple samples can be removed from a GBWT index # got: '127' # expected: '0' not ok 67 - unnamed test # got: '4' # expected: 'sample 2: 4 threads' not ok 68 - unnamed test # got: '2' # expected: 'sample 2: 2 haplotypes' not ok 69 - threads can be extracted from GBWT # got: '127' # expected: '0' not ok 70 - correct size for the thread file # got: '0' # expected: '121' not ok 71 - GBWTGraph construction # got: '127' # expected: '0' not ok 72 - unnamed test # got: '8e10d978d7303ba00ceed7837fcbd793' # expected: 'GBWTGraph was serialized correctly' not ok 73 - GBZ construction from GBWT # got: '127' # expected: '0' not ok 74 - unnamed test # got: '472cca17cf8f139dd590e78a8a6367bb' # expected: 'GBZ was serialized correctly' not ok 75 - GBZ construction from VCF # got: '127' # expected: '0' not ok 76 - Identical construction results from GBWT and VCF # got: '2' # expected: '0' not ok 77 - GBZ construction from GBWTGraph # got: '127' # expected: '0' not ok 78 - Identical construction results from XG and GBWTGraph # got: '2' # expected: '0' not ok 79 - GBWT extraction from GBZ # got: '127' # expected: '0' not ok 80 - Identical GBWT indexes # got: '2' # expected: '0' not ok 81 - GBWT + GBWTGraph extraction from GBZ # got: '127' # expected: '0' not ok 82 - Identical GBWT indexes # got: '2' # expected: '0' not ok 83 - Identical GBWTGraphs # got: '2' # expected: '0' not ok 84 - Path cover GBWTGraph construction # got: '127' # expected: '0' not ok 85 - unnamed test # got: '6a2738f51472e0ba1553a815a005b157' # expected: 'GBWTGraph was serialized correctly' not ok 86 - unnamed test # got: '32' # expected: 'path cover: 32 threads' not ok 87 - unnamed test # got: '2' # expected: 'path cover: 2 contigs' not ok 88 - unnamed test # got: '16' # expected: 'path cover: 16 haplotypes' not ok 89 - unnamed test # got: '16' # expected: 'path cover: 16 samples' not ok 90 - Path cover GBWTGraph construction # got: '127' # expected: '0' not ok 91 - unnamed test # got: '6a2738f51472e0ba1553a815a005b157' # expected: 'GBWTGraph was serialized correctly' not ok 92 - unnamed test # got: '34' # expected: 'path cover w/ paths: 34 threads' not ok 93 - unnamed test # got: '2' # expected: 'path cover w/ paths: 2 contigs' not ok 94 - unnamed test # got: '17' # expected: 'path cover w/ paths: 17 haplotypes' not ok 95 - unnamed test # got: '17' # expected: 'path cover w/ paths: 17 samples' not ok 96 - Local haplotypes GBWTGraph construction # got: '127' # expected: '0' not ok 97 - unnamed test # got: '00429586246711abcf1367a97d3c468c' # expected: 'GBWTGraph was serialized correctly' not ok 98 - unnamed test # got: '32' # expected: 'local haplotypes: 32 threads' not ok 99 - unnamed test # got: '2' # expected: 'local haplotypes: 2 contigs' not ok 100 - unnamed test # got: '16' # expected: 'local haplotypes: 16 haplotypes' not ok 101 - unnamed test # got: '16' # expected: 'local haplotypes: 16 samples' not ok 102 - Local haplotypes GBZ construction (single job) # got: '127' # expected: '0' not ok 103 - unnamed test # got: 'b6540312514c4e70aa45fc65b4bd762c' # expected: 'GBZ was serialized correctly' not ok 104 - Local haplotypes GBZ construction (two jobs) # got: '127' # expected: '0' not ok 105 - unnamed test # got: 'b6540312514c4e70aa45fc65b4bd762c' # expected: 'GBZ was serialized correctly' not ok 106 - Local haplotypes GBWTGraph construction # got: '127' # expected: '0' not ok 107 - unnamed test # got: '6a2738f51472e0ba1553a815a005b157' # expected: 'GBWTGraph was serialized correctly' not ok 108 - unnamed test # got: '34' # expected: 'local haplotypes w/ paths: 34 threads' not ok 109 - unnamed test # got: '2' # expected: 'local haplotypes w/ paths: 2 contigs' not ok 110 - unnamed test # got: '17' # expected: 'local haplotypes w/ paths: 17 haplotypes' not ok 111 - unnamed test # got: '17' # expected: 'local haplotypes w/ paths: 17 samples' not ok 112 - Local haplotypes with reference paths from a larger GBZ # got: '127' # expected: '0' not ok 113 - unnamed test # got: '36' # expected: 'local haplotypes w/ paths: 36 threads' not ok 114 - unnamed test # got: '2' # expected: 'local haplotypes w/ paths: 2 contigs' not ok 115 - unnamed test # got: '18' # expected: 'local haplotypes w/ paths: 18 haplotypes' not ok 116 - unnamed test # got: '18' # expected: 'local haplotypes w/ paths: 18 samples' not ok 117 - local haplotypes w/ paths: reference_samples set # got: '0' # expected: '1' not ok 118 - Augmented GBWTGraph construction # got: '127' # expected: '0' not ok 119 - unnamed test # got: '00429586246711abcf1367a97d3c468c' # expected: 'GBWTGraph was serialized correctly' not ok 120 - unnamed test # got: '18' # expected: 'augmented: 18 threads' not ok 121 - unnamed test # got: '2' # expected: 'augmented: 2 contigs' not ok 122 - unnamed test # got: '18' # expected: 'augmented: 18 haplotypes' not ok 123 - unnamed test # got: '17' # expected: 'augmented: 17 samples' not ok 124 - GBWT construction from GFA # got: '127' # expected: '0' not ok 125 - unnamed test # got: '44c27c37c7af6911c26aea2a41008460' # expected: 'GBWT was serialized correctly' not ok 126 - unnamed test # got: '4' # expected: 'gfa: 4 threads' not ok 127 - unnamed test # got: '2' # expected: 'gfa: 2 contigs' not ok 128 - unnamed test # got: '2' # expected: 'gfa: 2 haplotypes' not ok 129 - unnamed test # got: '1' # expected: 'gfa: 1 sample' not ok 130 - GBWT+GBWTGraph construction from GFA # got: '127' # expected: '0' not ok 131 - Identical construction results with and without GBWTGraph # got: '2' # expected: '0' not ok 132 - unnamed test # got: '5c1f16564c95b54f355972f065b25b4e' # expected: 'GBWTGraph was serialized correctly' not ok 133 - unnamed test # got: '0' # expected: 'no chopping: 0 translations' not ok 134 - GBZ construction from GFA # got: '127' # expected: '0' not ok 135 - unnamed test # got: 'ab241a3f79a781a367b701cb8888bf01' # expected: 'GBZ was serialized correctly' not ok 136 - GBWT+GBWTGraph construction from GFA with chopping # got: '127' # expected: '0' not ok 137 - unnamed test # got: '3' # expected: 'chopping: 3 threads' not ok 138 - unnamed test # got: '1' # expected: 'chopping: 1 contig' not ok 139 - unnamed test # got: '3' # expected: 'chopping: 3 haplotypes' not ok 140 - unnamed test # got: '2' # expected: 'chopping: 2 samples' not ok 141 - unnamed test # got: '9' # expected: 'chopping: 9 translations' not ok 142 - Translation can be extracted from GBZ # got: '127' # expected: '0' not ok 143 - unnamed test # got: '8' # expected: 'from GBZ: 8 translations' not ok 144 - GBWT+GBWTGraph construction from GFA with reference paths # got: '127' # expected: '0' not ok 145 - unnamed test # got: '6' # expected: 'ref paths: 6 threads' not ok 146 - unnamed test # got: '2' # expected: 'ref paths: 2 contigs' not ok 147 - unnamed test # got: '3' # expected: 'ref paths: 3 haplotypes' not ok 148 - unnamed test # got: '2' # expected: 'ref paths: 2 samples' not ok 149 - unnamed test # got: '0' # expected: 'ref paths: 0 translations' not ok 150 - GBZ construction from GFA with reference # got: '127' # expected: '0' not ok 151 - GBZ GBWT tag extraction works # got: '127' # expected: '0' not ok 152 - GBWT tags contain the correct reference samples # got: '' # expected: 'GRCh37 GRCh38' not ok 153 - GBZ GBWT tag modification works # got: '127' # expected: '0' not ok 154 - Changing reference_samples tag can make a reference a haplotype # got: '0' # expected: '1' not ok 155 - Changing reference_samples tag can make a haplotype a reference # got: '0' # expected: '1' not ok 156 - GBZ GBWT tag modification validation works # got: '127' # expected: '1' not ok 157 - Samples can be direcly set as references # got: '127' # expected: '0' not ok 158 - Direct reference assignment works # got: '' # expected: 'GRCh37 CHM13' not ok 159 - GBZ can represent reference paths without haplotype numbers # got: '0' # expected: '2' Failed 159/159 subtests t/38_vg_prune.t: line 13: vg: command not found t/38_vg_prune.t: line 16: vg: command not found t/38_vg_prune.t: line 17: vg: command not found t/38_vg_prune.t: line 18: vg: command not found t/38_vg_prune.t: line 19: vg: command not found t/38_vg_prune.t: line 23: vg: command not found t/38_vg_prune.t: line 24: vg: command not found t/38_vg_prune.t: line 25: vg: command not found t/38_vg_prune.t: line 26: vg: command not found t/38_vg_prune.t: line 30: vg: command not found t/38_vg_prune.t: line 31: vg: command not found t/38_vg_prune.t: line 32: vg: command not found t/38_vg_prune.t: line 33: vg: command not found t/38_vg_prune.t: line 37: vg: command not found t/38_vg_prune.t: line 38: vg: command not found t/38_vg_prune.t: line 39: vg: command not found t/38_vg_prune.t: line 40: vg: command not found t/38_vg_prune.t: line 44: vg: command not found t/38_vg_prune.t: line 45: vg: command not found t/38_vg_prune.t: line 46: vg: command not found t/38_vg_prune.t: line 47: vg: command not found t/38_vg_prune.t: line 56: vg: command not found t/38_vg_prune.t: line 57: vg: command not found t/38_vg_prune.t: line 58: vg: command not found t/38_vg_prune.t: line 61: vg: command not found t/38_vg_prune.t: line 62: vg: command not found t/38_vg_prune.t: line 63: vg: command not found t/38_vg_prune.t: line 64: vg: command not found t/38_vg_prune.t: line 65: vg: command not found head: cannot open 'xy.mapping' for reading: No such file or directory t/38_vg_prune.t: line 69: vg: command not found head: cannot open 'xy.mapping' for reading: No such file or directory t/38_vg_prune.t: line 71: vg: command not found head: cannot open 'xy.mapping' for reading: No such file or directory t/38_vg_prune.t ....... 1..21 not ok 1 - pruning produces the correct number of components # got: '0' # expected: '5' not ok 2 - unnamed test # got: '51' # expected: 'pruning leaves the correct number of nodes' not ok 3 - unnamed test # got: '51' # expected: 'pruning leaves the correct number of edges' not ok 4 - pruning without high-degree nodes produces the correct number of components # got: '0' # expected: '6' not ok 5 - unnamed test # got: '50' # expected: 'pruning without high-degree nodes leaves the correct number of nodes' not ok 6 - unnamed test # got: '47' # expected: 'pruning without high-degree nodes leaves the correct number of edges' not ok 7 - pruning with path restoring produces the correct number of components # got: '0' # expected: '1' not ok 8 - unnamed test # got: '64' # expected: 'pruning with path restoring leaves the correct number of nodes' not ok 9 - unnamed test # got: '68' # expected: 'pruning with path restoring leaves the correct number of edges' not ok 10 - pruning with path/thread unfolding produces the correct number of components # got: '0' # expected: '1' not ok 11 - unnamed test # got: '80' # expected: 'pruning with path/thread unfolding produces the correct number of nodes' not ok 12 - unnamed test # got: '92' # expected: 'pruning with path/thread unfolding produces the correct number of edges' not ok 13 - pruning with path unfolding produces the correct number of components # got: '0' # expected: '1' not ok 14 - unnamed test # got: '64' # expected: 'pruning with path unfolding produces the correct number of nodes' not ok 15 - unnamed test # got: '68' # expected: 'pruning with path unfolding produces the correct number of edges' not ok 16 - unfolding with multi-chromosome GBWT produces the correct number of components # got: '0' # expected: '1' not ok 17 - unnamed test # got: '80' # expected: 'unfolding with multi-chromosome GBWT produces the correct number of nodes' not ok 18 - unnamed test # got: '92' # expected: 'unfolding with multi-chromosome GBWT produces the correct number of edges' not ok 19 - unnamed test # got: '139_0_139_0_' # expected: 'empty mapping starts from the right node id' not ok 20 - unnamed test # got: '139_0_168_0_' # expected: 'the first unfolded graph adds the correct number of nodes to the mapping' not ok 21 - unnamed test # got: '139_0_196_0_' # expected: 'the second unfolded graph adds the correct number of nodes to the mapping' Failed 21/21 subtests t/39_vg_inject.t: line 11: vg: command not found t/39_vg_inject.t: line 12: vg: command not found t/39_vg_inject.t: line 13: vg: command not found t/39_vg_inject.t: line 14: vg: command not found t/39_vg_inject.t: line 22: vg: command not found t/39_vg_inject.t: line 22: vg: command not found t/39_vg_inject.t: line 25: vg: command not found t/39_vg_inject.t: line 25: vg: command not found t/39_vg_inject.t: line 25: vg: command not found t/39_vg_inject.t: line 28: vg: command not found t/39_vg_inject.t: line 28: vg: command not found [main_samview] fail to read the header from "-". t/39_vg_inject.t: line 31: vg: command not found t/39_vg_inject.t: line 31: vg: command not found [main_samview] fail to read the header from "-". t/39_vg_inject.t: line 34: vg: command not found t/39_vg_inject.t: line 34: vg: command not found [main_samview] fail to read the header from "-". t/39_vg_inject.t: line 37: vg: command not found t/39_vg_inject.t: line 37: vg: command not found [main_samview] fail to read the header from "-". t/39_vg_inject.t: line 40: vg: command not found t/39_vg_inject.t: line 40: vg: command not found [main_samview] fail to read the header from "-". t/39_vg_inject.t: line 43: vg: command not found t/39_vg_inject.t: line 43: vg: command not found [main_samview] fail to read the header from "-". t/39_vg_inject.t: line 46: vg: command not found t/39_vg_inject.t: line 46: vg: command not found t/39_vg_inject.t: line 48: vg: command not found t/39_vg_inject.t: line 48: vg: command not found t/39_vg_inject.t: line 52: vg: command not found t/39_vg_inject.t: line 52: vg: command not found t/39_vg_inject.t: line 55: vg: command not found t/39_vg_inject.t: line 59: vg: command not found rm: cannot remove 'j.xg': No such file or directory rm: cannot remove 'x.gcsa': No such file or directory rm: cannot remove 'x.gcsa.lcp': No such file or directory rm: cannot remove 'x.xg': No such file or directory t/39_vg_inject.t ...... 1..14 not ok 1 - reads are generated # got: '0' # expected: '1000' not ok 2 - vg inject works for all reads included in the original bam # got: '0' # expected: '1000' not ok 3 - vg inject retains read names # got: 'small/x.fa.fastq.000000000 # small/x.fa.fastq.000000001 # small/x.fa.fastq.000000002 # small/x.fa.fastq.000000003 # small/x.fa.fastq.000000004 # small/x.fa.fastq.000000005 # small/x.fa.fastq.000000006 # small/x.fa.fastq.000000007 # small/x.fa.fastq.000000008 # small/x.fa.fastq.000000009 # small/x.fa.fastq.000000010 # small/x.fa.fastq.000000011 # small/x.fa.fastq.000000012 # small/x.fa.fastq.000000013 # small/x.fa.fastq.000000014 # small/x.fa.fastq.000000015 # small/x.fa.fastq.000000016 # small/x.fa.fastq.000000017 # small/x.fa.fastq.000000018 # small/x.fa.fastq.000000019 # small/x.fa.fastq.000000020 # small/x.fa.fastq.000000021 # small/x.fa.fastq.000000022 # small/x.fa.fastq.000000023 # small/x.fa.fastq.000000024 # small/x.fa.fastq.000000025 # small/x.fa.fastq.000000026 # small/x.fa.fastq.000000027 # small/x.fa.fastq.000000028 # small/x.fa.fastq.000000029 # small/x.fa.fastq.000000030 # 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small/x.fa.fastq.000000677 # small/x.fa.fastq.000000678 # small/x.fa.fastq.000000679 # small/x.fa.fastq.000000680 # small/x.fa.fastq.000000681 # small/x.fa.fastq.000000682 # small/x.fa.fastq.000000683 # small/x.fa.fastq.000000684 # small/x.fa.fastq.000000685 # small/x.fa.fastq.000000686 # small/x.fa.fastq.000000687 # small/x.fa.fastq.000000688 # small/x.fa.fastq.000000689 # small/x.fa.fastq.000000690 # small/x.fa.fastq.000000691 # small/x.fa.fastq.000000692 # small/x.fa.fastq.000000693 # small/x.fa.fastq.000000694 # small/x.fa.fastq.000000695 # small/x.fa.fastq.000000696 # small/x.fa.fastq.000000697 # small/x.fa.fastq.000000698 # small/x.fa.fastq.000000699 # small/x.fa.fastq.000000700 # small/x.fa.fastq.000000701 # small/x.fa.fastq.000000702 # small/x.fa.fastq.000000703 # small/x.fa.fastq.000000704 # small/x.fa.fastq.000000705 # small/x.fa.fastq.000000706 # small/x.fa.fastq.000000707 # small/x.fa.fastq.000000708 # small/x.fa.fastq.000000709 # small/x.fa.fastq.000000710 # small/x.fa.fastq.000000711 # small/x.fa.fastq.000000712 # small/x.fa.fastq.000000713 # small/x.fa.fastq.000000714 # small/x.fa.fastq.000000715 # small/x.fa.fastq.000000716 # small/x.fa.fastq.000000717 # small/x.fa.fastq.000000718 # small/x.fa.fastq.000000719 # small/x.fa.fastq.000000720 # small/x.fa.fastq.000000721 # small/x.fa.fastq.000000722 # small/x.fa.fastq.000000723 # small/x.fa.fastq.000000724 # small/x.fa.fastq.000000725 # small/x.fa.fastq.000000726 # small/x.fa.fastq.000000727 # small/x.fa.fastq.000000728 # small/x.fa.fastq.000000729 # small/x.fa.fastq.000000730 # small/x.fa.fastq.000000731 # small/x.fa.fastq.000000732 # small/x.fa.fastq.000000733 # small/x.fa.fastq.000000734 # small/x.fa.fastq.000000735 # small/x.fa.fastq.000000736 # small/x.fa.fastq.000000737 # small/x.fa.fastq.000000738 # small/x.fa.fastq.000000739 # small/x.fa.fastq.000000740 # small/x.fa.fastq.000000741 # small/x.fa.fastq.000000742 # small/x.fa.fastq.000000743 # small/x.fa.fastq.000000744 # small/x.fa.fastq.000000745 # small/x.fa.fastq.000000746 # small/x.fa.fastq.000000747 # small/x.fa.fastq.000000748 # small/x.fa.fastq.000000749 # small/x.fa.fastq.000000750 # small/x.fa.fastq.000000751 # small/x.fa.fastq.000000752 # small/x.fa.fastq.000000753 # small/x.fa.fastq.000000754 # small/x.fa.fastq.000000755 # small/x.fa.fastq.000000756 # small/x.fa.fastq.000000757 # small/x.fa.fastq.000000758 # small/x.fa.fastq.000000759 # small/x.fa.fastq.000000760 # small/x.fa.fastq.000000761 # small/x.fa.fastq.000000762 # small/x.fa.fastq.000000763 # small/x.fa.fastq.000000764 # small/x.fa.fastq.000000765 # small/x.fa.fastq.000000766 # small/x.fa.fastq.000000767 # small/x.fa.fastq.000000768 # small/x.fa.fastq.000000769 # small/x.fa.fastq.000000770 # small/x.fa.fastq.000000771 # small/x.fa.fastq.000000772 # small/x.fa.fastq.000000773 # small/x.fa.fastq.000000774 # small/x.fa.fastq.000000775 # small/x.fa.fastq.000000776 # small/x.fa.fastq.000000777 # small/x.fa.fastq.000000778 # small/x.fa.fastq.000000779 # small/x.fa.fastq.000000780 # small/x.fa.fastq.000000781 # small/x.fa.fastq.000000782 # small/x.fa.fastq.000000783 # small/x.fa.fastq.000000784 # small/x.fa.fastq.000000785 # small/x.fa.fastq.000000786 # small/x.fa.fastq.000000787 # small/x.fa.fastq.000000788 # small/x.fa.fastq.000000789 # small/x.fa.fastq.000000790 # small/x.fa.fastq.000000791 # small/x.fa.fastq.000000792 # small/x.fa.fastq.000000793 # small/x.fa.fastq.000000794 # small/x.fa.fastq.000000795 # small/x.fa.fastq.000000796 # small/x.fa.fastq.000000797 # small/x.fa.fastq.000000798 # small/x.fa.fastq.000000799 # small/x.fa.fastq.000000800 # small/x.fa.fastq.000000801 # small/x.fa.fastq.000000802 # small/x.fa.fastq.000000803 # small/x.fa.fastq.000000804 # small/x.fa.fastq.000000805 # small/x.fa.fastq.000000806 # small/x.fa.fastq.000000807 # small/x.fa.fastq.000000808 # small/x.fa.fastq.000000809 # small/x.fa.fastq.000000810 # small/x.fa.fastq.000000811 # small/x.fa.fastq.000000812 # small/x.fa.fastq.000000813 # small/x.fa.fastq.000000814 # small/x.fa.fastq.000000815 # small/x.fa.fastq.000000816 # small/x.fa.fastq.000000817 # small/x.fa.fastq.000000818 # small/x.fa.fastq.000000819 # small/x.fa.fastq.000000820 # small/x.fa.fastq.000000821 # small/x.fa.fastq.000000822 # small/x.fa.fastq.000000823 # small/x.fa.fastq.000000824 # small/x.fa.fastq.000000825 # small/x.fa.fastq.000000826 # small/x.fa.fastq.000000827 # small/x.fa.fastq.000000828 # small/x.fa.fastq.000000829 # small/x.fa.fastq.000000830 # small/x.fa.fastq.000000831 # small/x.fa.fastq.000000832 # small/x.fa.fastq.000000833 # small/x.fa.fastq.000000834 # small/x.fa.fastq.000000835 # small/x.fa.fastq.000000836 # small/x.fa.fastq.000000837 # small/x.fa.fastq.000000838 # small/x.fa.fastq.000000839 # small/x.fa.fastq.000000840 # small/x.fa.fastq.000000841 # small/x.fa.fastq.000000842 # small/x.fa.fastq.000000843 # small/x.fa.fastq.000000844 # small/x.fa.fastq.000000845 # small/x.fa.fastq.000000846 # small/x.fa.fastq.000000847 # small/x.fa.fastq.000000848 # small/x.fa.fastq.000000849 # small/x.fa.fastq.000000850 # small/x.fa.fastq.000000851 # small/x.fa.fastq.000000852 # small/x.fa.fastq.000000853 # small/x.fa.fastq.000000854 # small/x.fa.fastq.000000855 # small/x.fa.fastq.000000856 # small/x.fa.fastq.000000857 # small/x.fa.fastq.000000858 # small/x.fa.fastq.000000859 # small/x.fa.fastq.000000860 # small/x.fa.fastq.000000861 # small/x.fa.fastq.000000862 # small/x.fa.fastq.000000863 # small/x.fa.fastq.000000864 # small/x.fa.fastq.000000865 # small/x.fa.fastq.000000866 # small/x.fa.fastq.000000867 # small/x.fa.fastq.000000868 # small/x.fa.fastq.000000869 # small/x.fa.fastq.000000870 # small/x.fa.fastq.000000871 # small/x.fa.fastq.000000872 # small/x.fa.fastq.000000873 # small/x.fa.fastq.000000874 # small/x.fa.fastq.000000875 # small/x.fa.fastq.000000876 # small/x.fa.fastq.000000877 # small/x.fa.fastq.000000878 # small/x.fa.fastq.000000879 # small/x.fa.fastq.000000880 # small/x.fa.fastq.000000881 # small/x.fa.fastq.000000882 # small/x.fa.fastq.000000883 # small/x.fa.fastq.000000884 # small/x.fa.fastq.000000885 # small/x.fa.fastq.000000886 # small/x.fa.fastq.000000887 # small/x.fa.fastq.000000888 # small/x.fa.fastq.000000889 # small/x.fa.fastq.000000890 # small/x.fa.fastq.000000891 # small/x.fa.fastq.000000892 # small/x.fa.fastq.000000893 # small/x.fa.fastq.000000894 # small/x.fa.fastq.000000895 # small/x.fa.fastq.000000896 # small/x.fa.fastq.000000897 # small/x.fa.fastq.000000898 # small/x.fa.fastq.000000899 # small/x.fa.fastq.000000900 # small/x.fa.fastq.000000901 # small/x.fa.fastq.000000902 # small/x.fa.fastq.000000903 # small/x.fa.fastq.000000904 # small/x.fa.fastq.000000905 # small/x.fa.fastq.000000906 # small/x.fa.fastq.000000907 # small/x.fa.fastq.000000908 # small/x.fa.fastq.000000909 # small/x.fa.fastq.000000910 # small/x.fa.fastq.000000911 # small/x.fa.fastq.000000912 # small/x.fa.fastq.000000913 # small/x.fa.fastq.000000914 # small/x.fa.fastq.000000915 # small/x.fa.fastq.000000916 # small/x.fa.fastq.000000917 # small/x.fa.fastq.000000918 # small/x.fa.fastq.000000919 # small/x.fa.fastq.000000920 # small/x.fa.fastq.000000921 # small/x.fa.fastq.000000922 # small/x.fa.fastq.000000923 # small/x.fa.fastq.000000924 # small/x.fa.fastq.000000925 # small/x.fa.fastq.000000926 # small/x.fa.fastq.000000927 # small/x.fa.fastq.000000928 # small/x.fa.fastq.000000929 # small/x.fa.fastq.000000930 # small/x.fa.fastq.000000931 # small/x.fa.fastq.000000932 # small/x.fa.fastq.000000933 # small/x.fa.fastq.000000934 # small/x.fa.fastq.000000935 # small/x.fa.fastq.000000936 # small/x.fa.fastq.000000937 # small/x.fa.fastq.000000938 # small/x.fa.fastq.000000939 # small/x.fa.fastq.000000940 # small/x.fa.fastq.000000941 # small/x.fa.fastq.000000942 # small/x.fa.fastq.000000943 # small/x.fa.fastq.000000944 # small/x.fa.fastq.000000945 # small/x.fa.fastq.000000946 # small/x.fa.fastq.000000947 # small/x.fa.fastq.000000948 # small/x.fa.fastq.000000949 # small/x.fa.fastq.000000950 # small/x.fa.fastq.000000951 # small/x.fa.fastq.000000952 # small/x.fa.fastq.000000953 # small/x.fa.fastq.000000954 # small/x.fa.fastq.000000955 # small/x.fa.fastq.000000956 # small/x.fa.fastq.000000957 # small/x.fa.fastq.000000958 # small/x.fa.fastq.000000959 # small/x.fa.fastq.000000960 # small/x.fa.fastq.000000961 # small/x.fa.fastq.000000962 # small/x.fa.fastq.000000963 # small/x.fa.fastq.000000964 # small/x.fa.fastq.000000965 # small/x.fa.fastq.000000966 # small/x.fa.fastq.000000967 # small/x.fa.fastq.000000968 # small/x.fa.fastq.000000969 # small/x.fa.fastq.000000970 # small/x.fa.fastq.000000971 # small/x.fa.fastq.000000972 # small/x.fa.fastq.000000973 # small/x.fa.fastq.000000974 # small/x.fa.fastq.000000975 # small/x.fa.fastq.000000976 # small/x.fa.fastq.000000977 # small/x.fa.fastq.000000978 # small/x.fa.fastq.000000979 # small/x.fa.fastq.000000980 # small/x.fa.fastq.000000981 # small/x.fa.fastq.000000982 # small/x.fa.fastq.000000983 # small/x.fa.fastq.000000984 # small/x.fa.fastq.000000985 # small/x.fa.fastq.000000986 # small/x.fa.fastq.000000987 # small/x.fa.fastq.000000988 # small/x.fa.fastq.000000989 # small/x.fa.fastq.000000990 # small/x.fa.fastq.000000991 # small/x.fa.fastq.000000992 # small/x.fa.fastq.000000993 # small/x.fa.fastq.000000994 # small/x.fa.fastq.000000995 # small/x.fa.fastq.000000996 # small/x.fa.fastq.000000997 # small/x.fa.fastq.000000998 # small/x.fa.fastq.000000999' # expected: '' not ok 4 - vg inject works perfectly for the position of alignment in the simple graph # got: '1 # 1 # 1 # 3 # 3 # 4 # 4 # 4 # 5 # 7 # 7 # 8 # 8 # 8 # 9 # 11 # 11 # 12 # 12 # 12 # 17 # 17 # 17 # 17 # 17 # 20 # 20 # 20 # 21 # 21 # 25 # 25 # 25 # 31 # 31 # 32 # 33 # 35 # 37 # 40 # 41 # 42 # 45 # 45 # 46 # 48 # 48 # 48 # 48 # 49 # 49 # 50 # 51 # 52 # 52 # 53 # 53 # 53 # 53 # 55 # 56 # 56 # 58 # 58 # 59 # 60 # 60 # 62 # 62 # 64 # 64 # 65 # 66 # 68 # 69 # 69 # 70 # 70 # 70 # 70 # 70 # 71 # 72 # 74 # 75 # 77 # 77 # 77 # 78 # 78 # 78 # 81 # 82 # 83 # 84 # 85 # 86 # 87 # 87 # 87 # 88 # 88 # 88 # 89 # 90 # 90 # 93 # 93 # 94 # 96 # 96 # 97 # 99 # 99 # 100 # 101 # 101 # 102 # 102 # 102 # 102 # 103 # 103 # 104 # 105 # 105 # 106 # 106 # 106 # 107 # 108 # 113 # 113 # 115 # 116 # 116 # 119 # 119 # 120 # 120 # 122 # 123 # 124 # 125 # 125 # 126 # 126 # 127 # 127 # 127 # 128 # 128 # 129 # 130 # 130 # 131 # 131 # 131 # 132 # 134 # 134 # 135 # 136 # 136 # 137 # 137 # 137 # 139 # 140 # 141 # 142 # 142 # 142 # 143 # 143 # 144 # 144 # 145 # 145 # 146 # 147 # 147 # 149 # 150 # 153 # 153 # 154 # 154 # 155 # 156 # 156 # 156 # 157 # 158 # 158 # 158 # 158 # 164 # 164 # 164 # 164 # 165 # 166 # 167 # 167 # 167 # 167 # 168 # 168 # 169 # 170 # 171 # 172 # 172 # 173 # 174 # 175 # 175 # 175 # 177 # 177 # 177 # 178 # 178 # 178 # 178 # 180 # 182 # 183 # 183 # 184 # 184 # 186 # 187 # 188 # 189 # 191 # 193 # 194 # 195 # 197 # 197 # 197 # 197 # 198 # 200 # 200 # 201 # 204 # 205 # 205 # 206 # 207 # 208 # 209 # 210 # 213 # 214 # 214 # 215 # 215 # 216 # 217 # 218 # 218 # 219 # 219 # 219 # 221 # 224 # 224 # 224 # 229 # 229 # 232 # 232 # 232 # 233 # 234 # 234 # 234 # 234 # 237 # 237 # 237 # 238 # 239 # 240 # 240 # 243 # 244 # 245 # 246 # 247 # 250 # 251 # 253 # 253 # 255 # 258 # 258 # 260 # 262 # 265 # 266 # 267 # 268 # 268 # 270 # 270 # 270 # 272 # 273 # 273 # 274 # 274 # 274 # 275 # 276 # 276 # 277 # 277 # 280 # 282 # 283 # 284 # 285 # 285 # 286 # 287 # 287 # 288 # 288 # 289 # 290 # 290 # 291 # 291 # 291 # 291 # 293 # 294 # 294 # 297 # 297 # 298 # 298 # 298 # 300 # 300 # 304 # 306 # 306 # 306 # 307 # 308 # 308 # 308 # 309 # 309 # 310 # 311 # 311 # 312 # 312 # 312 # 313 # 313 # 313 # 314 # 314 # 314 # 315 # 316 # 317 # 319 # 320 # 322 # 323 # 323 # 325 # 325 # 326 # 327 # 332 # 334 # 334 # 334 # 334 # 335 # 336 # 336 # 339 # 339 # 340 # 343 # 344 # 344 # 344 # 345 # 345 # 347 # 347 # 350 # 350 # 351 # 353 # 357 # 357 # 357 # 358 # 358 # 359 # 363 # 363 # 364 # 365 # 365 # 366 # 366 # 367 # 370 # 372 # 373 # 373 # 373 # 375 # 375 # 377 # 379 # 379 # 380 # 380 # 381 # 383 # 385 # 386 # 387 # 389 # 390 # 390 # 391 # 394 # 396 # 399 # 399 # 400 # 400 # 401 # 403 # 403 # 404 # 404 # 404 # 405 # 406 # 406 # 407 # 407 # 408 # 411 # 412 # 412 # 414 # 414 # 415 # 415 # 417 # 418 # 421 # 423 # 425 # 425 # 425 # 425 # 425 # 425 # 425 # 426 # 426 # 427 # 427 # 427 # 428 # 429 # 429 # 430 # 430 # 430 # 430 # 431 # 432 # 433 # 434 # 434 # 435 # 436 # 439 # 440 # 441 # 442 # 443 # 447 # 447 # 448 # 449 # 449 # 450 # 451 # 451 # 452 # 453 # 453 # 453 # 454 # 455 # 455 # 456 # 457 # 458 # 458 # 460 # 460 # 460 # 460 # 462 # 462 # 464 # 464 # 465 # 465 # 466 # 466 # 466 # 467 # 468 # 470 # 471 # 471 # 471 # 471 # 471 # 472 # 473 # 473 # 473 # 474 # 477 # 477 # 478 # 478 # 478 # 480 # 480 # 481 # 482 # 483 # 483 # 483 # 484 # 484 # 484 # 487 # 488 # 490 # 491 # 492 # 493 # 493 # 493 # 494 # 494 # 495 # 497 # 500 # 500 # 501 # 501 # 502 # 503 # 504 # 505 # 506 # 506 # 508 # 508 # 510 # 511 # 514 # 515 # 516 # 516 # 518 # 520 # 521 # 522 # 522 # 523 # 523 # 525 # 525 # 525 # 526 # 527 # 527 # 528 # 530 # 530 # 531 # 532 # 533 # 535 # 537 # 537 # 537 # 538 # 539 # 542 # 544 # 545 # 546 # 546 # 547 # 549 # 549 # 551 # 551 # 552 # 552 # 552 # 553 # 554 # 554 # 556 # 557 # 558 # 558 # 560 # 561 # 563 # 565 # 565 # 566 # 567 # 567 # 569 # 569 # 569 # 570 # 571 # 572 # 572 # 572 # 572 # 573 # 575 # 577 # 578 # 579 # 581 # 582 # 584 # 584 # 585 # 585 # 588 # 589 # 590 # 593 # 593 # 595 # 596 # 597 # 598 # 599 # 600 # 600 # 600 # 600 # 601 # 601 # 602 # 602 # 603 # 604 # 605 # 605 # 606 # 608 # 608 # 608 # 609 # 611 # 612 # 612 # 613 # 613 # 614 # 614 # 615 # 615 # 615 # 616 # 618 # 618 # 619 # 619 # 620 # 620 # 620 # 622 # 625 # 625 # 626 # 626 # 627 # 628 # 629 # 629 # 630 # 630 # 630 # 631 # 632 # 632 # 634 # 634 # 634 # 636 # 636 # 636 # 637 # 637 # 639 # 639 # 639 # 641 # 642 # 642 # 644 # 644 # 645 # 649 # 650 # 650 # 651 # 654 # 655 # 656 # 656 # 657 # 658 # 660 # 661 # 661 # 663 # 667 # 668 # 668 # 671 # 672 # 674 # 674 # 674 # 675 # 676 # 676 # 676 # 676 # 677 # 677 # 680 # 681 # 683 # 684 # 684 # 687 # 688 # 690 # 692 # 693 # 693 # 693 # 696 # 697 # 697 # 700 # 700 # 701 # 702 # 702 # 702 # 703 # 703 # 704 # 704 # 704 # 704 # 705 # 706 # 706 # 707 # 707 # 711 # 713 # 713 # 714 # 718 # 720 # 722 # 723 # 724 # 724 # 724 # 725 # 726 # 726 # 726 # 728 # 729 # 729 # 730 # 733 # 734 # 734 # 735 # 738 # 738 # 738 # 741 # 743 # 746 # 747 # 749 # 751 # 752 # 752 # 753 # 754 # 755 # 756 # 758 # 758 # 759 # 759 # 760 # 761 # 761 # 762 # 763 # 763 # 764 # 765 # 767 # 767 # 768 # 769 # 770 # 770 # 770 # 771 # 771 # 771 # 775 # 776 # 776 # 777 # 779 # 779 # 779 # 779 # 781 # 781 # 782 # 785 # 787 # 787 # 787 # 788 # 789 # 789 # 790 # 790 # 791 # 791 # 792 # 792 # 792 # 793 # 793 # 793 # 794 # 796 # 796 # 802 # 806 # 806 # 807 # 808 # 809 # 809 # 809 # 810 # 810 # 812 # 813 # 818 # 825 # 825 # 826 # 826 # 827 # 827 # 828 # 829 # 830 # 830 # 834 # 834 # 835 # 835 # 836 # 837 # 841 # 844 # 845 # 845 # 845 # 845 # 846 # 846 # 850 # 850 # 852 # 853 # 853 # 854 # 855 # 856 # 858 # 859 # 860 # 861 # 862 # 862 # 863 # 864 # 866 # 869 # 870 # 870 # 871 # 873 # 874 # 874 # 876 # 877 # 877 # 877 # 877 # 879 # 881 # 882 # 883 # 884 # 885 # 885 # 885 # 886 # 887 # 888 # 889 # 889 # 889 # 889 # 889 # 890 # 890 # 890 # 890 # 891 # 892 # 892 # 892 # 895 # 895 # 895 # 896 # 896 # 896 # 896 # 896 # 897 # 898 # 898 # 898 # 899 # 900 # 900 # 901' # expected: '' not ok 5 - vg inject works perfectly for the position of alignment # got: '1 # 1 # 1 # 3 # 3 # 4 # 4 # 4 # 5 # 7 # 7 # 8 # 8 # 8 # 9 # 11 # 11 # 12 # 12 # 12 # 17 # 17 # 17 # 17 # 17 # 20 # 20 # 20 # 21 # 21 # 25 # 25 # 25 # 31 # 31 # 32 # 33 # 35 # 37 # 40 # 41 # 42 # 45 # 45 # 46 # 48 # 48 # 48 # 48 # 49 # 49 # 50 # 51 # 52 # 52 # 53 # 53 # 53 # 53 # 55 # 56 # 56 # 58 # 58 # 59 # 60 # 60 # 62 # 62 # 64 # 64 # 65 # 66 # 68 # 69 # 69 # 70 # 70 # 70 # 70 # 70 # 71 # 72 # 74 # 75 # 77 # 77 # 77 # 78 # 78 # 78 # 81 # 82 # 83 # 84 # 85 # 86 # 87 # 87 # 87 # 88 # 88 # 88 # 89 # 90 # 90 # 93 # 93 # 94 # 96 # 96 # 97 # 99 # 99 # 100 # 101 # 101 # 102 # 102 # 102 # 102 # 103 # 103 # 104 # 105 # 105 # 106 # 106 # 106 # 107 # 108 # 113 # 113 # 115 # 116 # 116 # 119 # 119 # 120 # 120 # 122 # 123 # 124 # 125 # 125 # 126 # 126 # 127 # 127 # 127 # 128 # 128 # 129 # 130 # 130 # 131 # 131 # 131 # 132 # 134 # 134 # 135 # 136 # 136 # 137 # 137 # 137 # 139 # 140 # 141 # 142 # 142 # 142 # 143 # 143 # 144 # 144 # 145 # 145 # 146 # 147 # 147 # 149 # 150 # 153 # 153 # 154 # 154 # 155 # 156 # 156 # 156 # 157 # 158 # 158 # 158 # 158 # 164 # 164 # 164 # 164 # 165 # 166 # 167 # 167 # 167 # 167 # 168 # 168 # 169 # 170 # 171 # 172 # 172 # 173 # 174 # 175 # 175 # 175 # 177 # 177 # 177 # 178 # 178 # 178 # 178 # 180 # 182 # 183 # 183 # 184 # 184 # 186 # 187 # 188 # 189 # 191 # 193 # 194 # 195 # 197 # 197 # 197 # 197 # 198 # 200 # 200 # 201 # 204 # 205 # 205 # 206 # 207 # 208 # 209 # 210 # 213 # 214 # 214 # 215 # 215 # 216 # 217 # 218 # 218 # 219 # 219 # 219 # 221 # 224 # 224 # 224 # 229 # 229 # 232 # 232 # 232 # 233 # 234 # 234 # 234 # 234 # 237 # 237 # 237 # 238 # 239 # 240 # 240 # 243 # 244 # 245 # 246 # 247 # 250 # 251 # 253 # 253 # 255 # 258 # 258 # 260 # 262 # 265 # 266 # 267 # 268 # 268 # 270 # 270 # 270 # 272 # 273 # 273 # 274 # 274 # 274 # 275 # 276 # 276 # 277 # 277 # 280 # 282 # 283 # 284 # 285 # 285 # 286 # 287 # 287 # 288 # 288 # 289 # 290 # 290 # 291 # 291 # 291 # 291 # 293 # 294 # 294 # 297 # 297 # 298 # 298 # 298 # 300 # 300 # 304 # 306 # 306 # 306 # 307 # 308 # 308 # 308 # 309 # 309 # 310 # 311 # 311 # 312 # 312 # 312 # 313 # 313 # 313 # 314 # 314 # 314 # 315 # 316 # 317 # 319 # 320 # 322 # 323 # 323 # 325 # 325 # 326 # 327 # 332 # 334 # 334 # 334 # 334 # 335 # 336 # 336 # 339 # 339 # 340 # 343 # 344 # 344 # 344 # 345 # 345 # 347 # 347 # 350 # 350 # 351 # 353 # 357 # 357 # 357 # 358 # 358 # 359 # 363 # 363 # 364 # 365 # 365 # 366 # 366 # 367 # 370 # 372 # 373 # 373 # 373 # 375 # 375 # 377 # 379 # 379 # 380 # 380 # 381 # 383 # 385 # 386 # 387 # 389 # 390 # 390 # 391 # 394 # 396 # 399 # 399 # 400 # 400 # 401 # 403 # 403 # 404 # 404 # 404 # 405 # 406 # 406 # 407 # 407 # 408 # 411 # 412 # 412 # 414 # 414 # 415 # 415 # 417 # 418 # 421 # 423 # 425 # 425 # 425 # 425 # 425 # 425 # 425 # 426 # 426 # 427 # 427 # 427 # 428 # 429 # 429 # 430 # 430 # 430 # 430 # 431 # 432 # 433 # 434 # 434 # 435 # 436 # 439 # 440 # 441 # 442 # 443 # 447 # 447 # 448 # 449 # 449 # 450 # 451 # 451 # 452 # 453 # 453 # 453 # 454 # 455 # 455 # 456 # 457 # 458 # 458 # 460 # 460 # 460 # 460 # 462 # 462 # 464 # 464 # 465 # 465 # 466 # 466 # 466 # 467 # 468 # 470 # 471 # 471 # 471 # 471 # 471 # 472 # 473 # 473 # 473 # 474 # 477 # 477 # 478 # 478 # 478 # 480 # 480 # 481 # 482 # 483 # 483 # 483 # 484 # 484 # 484 # 487 # 488 # 490 # 491 # 492 # 493 # 493 # 493 # 494 # 494 # 495 # 497 # 500 # 500 # 501 # 501 # 502 # 503 # 504 # 505 # 506 # 506 # 508 # 508 # 510 # 511 # 514 # 515 # 516 # 516 # 518 # 520 # 521 # 522 # 522 # 523 # 523 # 525 # 525 # 525 # 526 # 527 # 527 # 528 # 530 # 530 # 531 # 532 # 533 # 535 # 537 # 537 # 537 # 538 # 539 # 542 # 544 # 545 # 546 # 546 # 547 # 549 # 549 # 551 # 551 # 552 # 552 # 552 # 553 # 554 # 554 # 556 # 557 # 558 # 558 # 560 # 561 # 563 # 565 # 565 # 566 # 567 # 567 # 569 # 569 # 569 # 570 # 571 # 572 # 572 # 572 # 572 # 573 # 575 # 577 # 578 # 579 # 581 # 582 # 584 # 584 # 585 # 585 # 588 # 589 # 590 # 593 # 593 # 595 # 596 # 597 # 598 # 599 # 600 # 600 # 600 # 600 # 601 # 601 # 602 # 602 # 603 # 604 # 605 # 605 # 606 # 608 # 608 # 608 # 609 # 611 # 612 # 612 # 613 # 613 # 614 # 614 # 615 # 615 # 615 # 616 # 618 # 618 # 619 # 619 # 620 # 620 # 620 # 622 # 625 # 625 # 626 # 626 # 627 # 628 # 629 # 629 # 630 # 630 # 630 # 631 # 632 # 632 # 634 # 634 # 634 # 636 # 636 # 636 # 637 # 637 # 639 # 639 # 639 # 641 # 642 # 642 # 644 # 644 # 645 # 649 # 650 # 650 # 651 # 654 # 655 # 656 # 656 # 657 # 658 # 660 # 661 # 661 # 663 # 667 # 668 # 668 # 671 # 672 # 674 # 674 # 674 # 675 # 676 # 676 # 676 # 676 # 677 # 677 # 680 # 681 # 683 # 684 # 684 # 687 # 688 # 690 # 692 # 693 # 693 # 693 # 696 # 697 # 697 # 700 # 700 # 701 # 702 # 702 # 702 # 703 # 703 # 704 # 704 # 704 # 704 # 705 # 706 # 706 # 707 # 707 # 711 # 713 # 713 # 714 # 718 # 720 # 722 # 723 # 724 # 724 # 724 # 725 # 726 # 726 # 726 # 728 # 729 # 729 # 730 # 733 # 734 # 734 # 735 # 738 # 738 # 738 # 741 # 743 # 746 # 747 # 749 # 751 # 752 # 752 # 753 # 754 # 755 # 756 # 758 # 758 # 759 # 759 # 760 # 761 # 761 # 762 # 763 # 763 # 764 # 765 # 767 # 767 # 768 # 769 # 770 # 770 # 770 # 771 # 771 # 771 # 775 # 776 # 776 # 777 # 779 # 779 # 779 # 779 # 781 # 781 # 782 # 785 # 787 # 787 # 787 # 788 # 789 # 789 # 790 # 790 # 791 # 791 # 792 # 792 # 792 # 793 # 793 # 793 # 794 # 796 # 796 # 802 # 806 # 806 # 807 # 808 # 809 # 809 # 809 # 810 # 810 # 812 # 813 # 818 # 825 # 825 # 826 # 826 # 827 # 827 # 828 # 829 # 830 # 830 # 834 # 834 # 835 # 835 # 836 # 837 # 841 # 844 # 845 # 845 # 845 # 845 # 846 # 846 # 850 # 850 # 852 # 853 # 853 # 854 # 855 # 856 # 858 # 859 # 860 # 861 # 862 # 862 # 863 # 864 # 866 # 869 # 870 # 870 # 871 # 873 # 874 # 874 # 876 # 877 # 877 # 877 # 877 # 879 # 881 # 882 # 883 # 884 # 885 # 885 # 885 # 886 # 887 # 888 # 889 # 889 # 889 # 889 # 889 # 890 # 890 # 890 # 890 # 891 # 892 # 892 # 892 # 895 # 895 # 895 # 896 # 896 # 896 # 896 # 896 # 897 # 898 # 898 # 898 # 899 # 900 # 900 # 901' # expected: '' not ok 6 - vg inject works perfectly for the mapping quality of alignment # got: '1000' # expected: '0' not ok 7 - vg inject works perfectly for the cigar of alignment in the simple graph # got: '100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 19M1D81M # 24M1I75M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 62M1D32M1D6M # 100M # 100M # 60M1I39M # 100M # 100M # 60M1D40M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 52M1D42M1I5M # 14M1D86M # 19M1I80M # 100M # 100M # 100M # 79M1D21M # 100M # 100M # 100M # 100M # 100M # 9M1I90M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 56M1D22M1I21M # 100M # 100M # 100M # 29M1I70M # 100M # 34M1I65M # 16M1D84M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 75M1I24M # 100M # 100M # 73M1D27M # 100M # 100M # 52M1D48M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 21M1I78M # 100M # 100M # 3M1D97M # 100M # 100M # 8M1D92M # 100M # 67M1I32M # 48M1D52M # 100M # 100M # 100M # 100M # 100M # 100M # 78M1D22M # 100M # 100M # 100M # 100M # 15M1D85M # 94M1I5M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 10M1I89M # 100M # 100M # 100M # 100M # 100M # 22M1I77M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 26M1D74M # 100M # 100M # 100M # 100M # 100M # 100M # 12M1I64M1D23M # 100M # 100M # 100M # 28M1I71M # 5M1I94M # 100M # 100M # 100M # 100M # 3M1D97M # 83M1D10M1I6M # 80M1D20M # 100M # 100M # 100M # 100M # 100M # 79M1D10M1I10M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 7M1I92M # 100M # 39M1I60M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 3M1D64M1I32M # 59M1I40M # 100M # 100M # 100M # 100M # 60M1I39M # 63M1I36M # 100M # 29M1D43M1D28M # 100M # 100M # 100M # 33M1D67M # 100M # 100M # 100M # 100M # 55M1I44M # 100M # 100M # 100M # 46M1D54M # 100M # 100M # 100M # 100M # 8M1I91M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 58M1I41M # 100M # 100M # 100M # 100M # 100M # 100M # 36M1D64M # 100M # 100M # 100M # 100M # 100M # 100M # 85M1I14M # 100M # 86M1I13M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 39M1D61M # 100M # 86M1D14M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 67M1I32M # 100M # 61M1D39M # 100M # 100M # 100M # 100M # 100M # 100M # 17M1D26M1D57M # 100M # 100M # 100M # 100M # 100M # 4M1I95M # 100M # 100M # 100M # 35M1I64M # 100M # 13M1I86M # 100M # 46M1D54M # 44M1I55M # 74M1I25M # 100M # 100M # 100M # 8M1D19M1I72M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 84M1D16M # 100M # 100M # 100M # 100M # 100M # 64M1D36M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 57M1D43M # 14M1D86M # 100M # 100M # 28M1I71M # 100M # 100M # 100M # 31M1I68M # 100M # 100M # 100M # 86M1D14M # 100M # 45M1I54M # 100M # 100M # 100M # 100M # 86M1I13M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 91M1I8M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 35M1I64M # 100M # 100M # 100M # 56M1D44M # 100M # 13M1D45M1D42M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 39M1D61M # 100M # 100M # 100M # 15M1D85M # 100M # 100M # 100M # 42M1D58M # 100M # 100M # 100M # 100M # 100M # 100M # 41M1I58M # 100M # 100M # 100M # 100M # 24M1D76M # 49M1D51M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 48M1D52M # 68M1D32M # 39M1D51M1D10M # 100M # 100M # 100M # 9M1D91M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 68M1D32M # 100M # 100M # 100M # 50M1I49M # 100M # 100M # 100M # 63M1I17M1I18M # 5M1D95M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 9M1I90M # 100M # 40M1I59M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 72M1I27M # 100M # 100M # 100M # 100M # 100M # 61M1I38M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 85M1I14M # 100M # 100M # 93M1D7M # 100M # 100M # 43M1I9M1I46M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 82M1D18M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 61M1I38M # 49M1I50M # 100M # 100M # 100M # 100M # 28M1D72M # 100M # 100M # 23M1I76M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 68M1I6M1I24M # 100M # 100M # 100M # 100M # 100M # 100M # 45M1D55M # 100M # 43M1I39M1I16M # 100M # 93M1D7M # 66M1I33M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 58M1D42M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 64M1D36M # 100M # 100M # 59M1D41M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 66M1D34M # 94M1D6M # 100M # 100M # 100M # 46M1I53M # 100M # 48M1D52M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 50M1D50M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 57M1D13M1D18M1D12M # 84M1D16M # 61M1D39M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 28M1D72M # 100M # 100M # 100M # 100M # 100M # 100M # 86M1D14M # 100M # 100M # 100M # 95M5S # 100M # 100M # 100M # 100M # 22M1D78M # 100M # 100M # 100M # 2S98M # 100M # 100M # 95M1I4M # 100M # 95M1D5M # 100M # 76M1D24M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 5M1D69M1D26M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 86M1I13M # 100M # 100M # 65M1I34M # 100M # 100M # 100M # 100M # 100M # 18M1D82M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 37M1I62M # 100M # 100M # 100M # 67M1I32M # 100M # 100M # 100M # 100M # 100M # 58M1I41M # 28M1I71M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 4M1D96M # 69M1I30M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 16M1I32M1D51M # 100M # 100M # 100M # 84M1I15M # 100M # 100M # 12M1D88M # 100M # 35M1I64M # 100M # 100M # 100M # 100M # 100M # 100M # 49M1D51M # 100M # 100M # 100M # 100M # 14M1D86M # 68M1D32M # 27M1D73M # 100M # 100M # 71M1I28M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 90M1D10M # 100M # 100M # 35M1D65M # 100M # 4M1I61M1I33M # 100M # 100M # 100M # 100M # 9M1D91M # 100M # 100M # 100M # 100M # 100M # 100M # 66M1I33M # 100M # 50M1I49M # 100M # 100M # 100M # 100M # 100M # 38M1I52M1I8M # 100M # 100M # 100M # 45M1I54M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 7M1I92M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 27M1I72M # 100M # 100M # 100M # 100M # 100M # 100M # 84M1D16M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 37M1D63M # 100M # 100M # 43M1D18M1I38M # 100M # 100M # 100M # 100M # 100M # 100M # 68M1D32M # 88M1D12M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 8M1D24M1I67M # 88M1D12M # 100M # 100M # 100M # 50M1I49M # 44M1D56M # 100M # 56M1D44M # 100M # 34M1I65M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 49M1D51M # 100M # 100M # 100M # 100M # 100M # 100M # 42M1D58M # 35M1I64M # 100M # 100M # 100M # 100M # 24M1D76M # 76M1I23M # 100M # 100M # 68M1I31M # 100M # 100M # 6M1I93M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 34M1D66M # 31M1D69M # 100M # 100M # 100M # 100M # 100M # 100M # 15M1I84M # 100M # 100M # 100M # 5M1I94M # 100M # 100M # 100M # 100M # 100M # 50M1D50M # 100M # 100M # 64M1D36M # 100M # 96M1D4M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 25M1D75M # 85M1I14M # 48M1D52M # 100M # 100M # 21M1D79M # 100M # 100M # 100M # 100M # 100M # 100M # 9M1I90M # 100M # 100M # 100M # 100M # 100M # 90M1D10M # 100M' # expected: '' not ok 8 - vg inject works perfectly for the cigar of alignment # got: '100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 19M1D81M # 24M1I75M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 62M1D32M1D6M # 100M # 100M # 60M1I39M # 100M # 100M # 60M1D40M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 52M1D42M1I5M # 14M1D86M # 19M1I80M # 100M # 100M # 100M # 79M1D21M # 100M # 100M # 100M # 100M # 100M # 9M1I90M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 56M1D22M1I21M # 100M # 100M # 100M # 29M1I70M # 100M # 34M1I65M # 16M1D84M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 75M1I24M # 100M # 100M # 73M1D27M # 100M # 100M # 52M1D48M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 21M1I78M # 100M # 100M # 3M1D97M # 100M # 100M # 8M1D92M # 100M # 67M1I32M # 48M1D52M # 100M # 100M # 100M # 100M # 100M # 100M # 78M1D22M # 100M # 100M # 100M # 100M # 15M1D85M # 94M1I5M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 10M1I89M # 100M # 100M # 100M # 100M # 100M # 22M1I77M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 26M1D74M # 100M # 100M # 100M # 100M # 100M # 100M # 12M1I64M1D23M # 100M # 100M # 100M # 28M1I71M # 5M1I94M # 100M # 100M # 100M # 100M # 3M1D97M # 83M1D10M1I6M # 80M1D20M # 100M # 100M # 100M # 100M # 100M # 79M1D10M1I10M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 7M1I92M # 100M # 39M1I60M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 3M1D64M1I32M # 59M1I40M # 100M # 100M # 100M # 100M # 60M1I39M # 63M1I36M # 100M # 29M1D43M1D28M # 100M # 100M # 100M # 33M1D67M # 100M # 100M # 100M # 100M # 55M1I44M # 100M # 100M # 100M # 46M1D54M # 100M # 100M # 100M # 100M # 8M1I91M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 58M1I41M # 100M # 100M # 100M # 100M # 100M # 100M # 36M1D64M # 100M # 100M # 100M # 100M # 100M # 100M # 85M1I14M # 100M # 86M1I13M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 39M1D61M # 100M # 86M1D14M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 67M1I32M # 100M # 61M1D39M # 100M # 100M # 100M # 100M # 100M # 100M # 17M1D26M1D57M # 100M # 100M # 100M # 100M # 100M # 4M1I95M # 100M # 100M # 100M # 35M1I64M # 100M # 13M1I86M # 100M # 46M1D54M # 44M1I55M # 74M1I25M # 100M # 100M # 100M # 8M1D19M1I72M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 84M1D16M # 100M # 100M # 100M # 100M # 100M # 64M1D36M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 57M1D43M # 14M1D86M # 100M # 100M # 28M1I71M # 100M # 100M # 100M # 31M1I68M # 100M # 100M # 100M # 86M1D14M # 100M # 45M1I54M # 100M # 100M # 100M # 100M # 86M1I13M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 91M1I8M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 35M1I64M # 100M # 100M # 100M # 56M1D44M # 100M # 13M1D45M1D42M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 39M1D61M # 100M # 100M # 100M # 15M1D85M # 100M # 100M # 100M # 42M1D58M # 100M # 100M # 100M # 100M # 100M # 100M # 41M1I58M # 100M # 100M # 100M # 100M # 24M1D76M # 49M1D51M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 48M1D52M # 68M1D32M # 39M1D51M1D10M # 100M # 100M # 100M # 9M1D91M # 100M # 100M # 100M # 100M # 100M # 100M 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# 50M1I49M # 100M # 100M # 100M # 100M # 100M # 38M1I52M1I8M # 100M # 100M # 100M # 45M1I54M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 7M1I92M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 27M1I72M # 100M # 100M # 100M # 100M # 100M # 100M # 84M1D16M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 37M1D63M # 100M # 100M # 43M1D18M1I38M # 100M # 100M # 100M # 100M # 100M # 100M # 68M1D32M # 88M1D12M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 8M1D24M1I67M # 88M1D12M # 100M # 100M # 100M # 50M1I49M # 44M1D56M # 100M # 56M1D44M # 100M # 34M1I65M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 49M1D51M # 100M # 100M # 100M # 100M # 100M # 100M # 42M1D58M # 35M1I64M # 100M # 100M # 100M # 100M # 24M1D76M # 76M1I23M # 100M # 100M # 68M1I31M # 100M # 100M # 6M1I93M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 34M1D66M # 31M1D69M # 100M # 100M # 100M # 100M # 100M # 100M # 15M1I84M # 100M # 100M # 100M # 5M1I94M # 100M # 100M # 100M # 100M # 100M # 50M1D50M # 100M # 100M # 64M1D36M # 100M # 96M1D4M # 100M # 100M # 100M # 100M # 100M # 100M # 100M # 25M1D75M # 85M1I14M # 48M1D52M # 100M # 100M # 21M1D79M # 100M # 100M # 100M # 100M # 100M # 100M # 9M1I90M # 100M # 100M # 100M # 100M # 100M # 90M1D10M # 100M' # expected: '' not ok 9 - vg inject preserves all reads # got: '0' # expected: '470' ok 10 - vg inject works perfectly for the reads flagged as is_reverse ok 11 - vg inject does not make an alignment for an umapped read ok 12 - vg inject does not crash on an unmapped read not ok 13 - vg inject supports GAF output # got: '0' # expected: '1000' ok 14 - vg inject produces valid alignments of the read and reference Dubious, test returned 1 (wstat 256, 0x100) Failed 10/14 subtests t/40_vg_gamcompare.t: line 11: vg: command not found t/40_vg_gamcompare.t: line 12: vg: command not found t/40_vg_gamcompare.t: line 13: vg: command not found t/40_vg_gamcompare.t: line 14: vg: command not found t/40_vg_gamcompare.t: line 15: vg: command not found t/40_vg_gamcompare.t: line 17: vg: command not found t/40_vg_gamcompare.t: line 17: vg: command not found t/40_vg_gamcompare.t: line 17: vg: command not found t/40_vg_gamcompare.t: line 17: vg: command not found t/40_vg_gamcompare.t: line 19: vg: command not found t/40_vg_gamcompare.t: line 19: vg: command not found t/40_vg_gamcompare.t: line 22: vg: command not found t/40_vg_gamcompare.t: line 23: vg: command not found t/40_vg_gamcompare.t: line 24: vg: command not found t/40_vg_gamcompare.t: line 25: vg: command not found t/40_vg_gamcompare.t: line 26: vg: command not found t/40_vg_gamcompare.t: line 27: vg: command not found t/40_vg_gamcompare.t: line 29: vg: command not found t/40_vg_gamcompare.t: line 29: vg: command not found t/40_vg_gamcompare.t: line 30: vg: command not found t/40_vg_gamcompare.t: line 30: vg: command not found t/40_vg_gamcompare.t: line 31: vg: command not found t/40_vg_gamcompare.t: line 31: vg: command not found t/40_vg_gamcompare.t: line 32: vg: command not found t/40_vg_gamcompare.t: line 32: vg: command not found t/40_vg_gamcompare.t: line 33: vg: command not found t/40_vg_gamcompare.t: line 33: vg: command not found t/40_vg_gamcompare.t .. 1..7 not ok 1 - gamcompare completes # got: '0' # expected: '1000' not ok 2 - gamcompare says the truth is correctly mapped # got: '0' # expected: '1000' not ok 3 - Reads annotated with leftmost position only are close enough at a long distance # got: '0' # expected: '1' not ok 4 - Reads are close enough at a long distance with a distance index # got: '0' # expected: '1' ok 5 - Reads annotated with leftmost position only are too far apart at a short distance ok 6 - Reads are too far apart at a short distance with a distance index not ok 7 - Reads annotated with multiple positions only are close enough at a short distance # got: '0' # expected: '1' Failed 5/7 subtests t/41_vg_viz.t: line 11: vg: command not found t/41_vg_viz.t: line 12: vg: command not found t/41_vg_viz.t: line 13: vg: command not found t/41_vg_viz.t: line 13: vg: command not found t/41_vg_viz.t: line 13: vg: command not found t/41_vg_viz.t: line 15: vg: command not found wc: t.svg: No such file or directory (standard_in) 1: syntax error t/41_vg_viz.t: line 19: vg: command not found t/41_vg_viz.t: line 24: vg: command not found t/41_vg_viz.t ......... 1..4 not ok 1 - unnamed test # got: '1' # expected: 'vg viz runs' not ok 2 - vg viz succeeds when drawing a PNG # got: '127' # expected: '0' not ok 3 - vg viz actually creates an output PNG # got: '1' # expected: '0' not ok 4 - vg viz knows when a graph is too big to draw as a PNG # got: '127' # expected: '1' Failed 4/4 subtests t/42_vg_gamsort.t: line 11: vg: command not found t/42_vg_gamsort.t: line 12: vg: command not found t/42_vg_gamsort.t: line 13: vg: command not found t/42_vg_gamsort.t: line 15: vg: command not found t/42_vg_gamsort.t: line 17: vg: command not found t/42_vg_gamsort.t: line 18: vg: command not found t/42_vg_gamsort.t: line 22: vg: command not found t/42_vg_gamsort.t ..... 1..2 ok 1 - Sorting a GAM orders the alignments by min node ID not ok 2 - sorted GAMs can be indexed during the sort # got: '127' # expected: '0' Failed 1/2 subtests t/43_vg_simplify.t: line 10: vg: command not found t/43_vg_simplify.t: line 16: vg: command not found t/43_vg_simplify.t: line 16: vg: command not found t/43_vg_simplify.t: line 16: vg: command not found t/43_vg_simplify.t: line 18: vg: command not found t/43_vg_simplify.t: line 21: vg: command not found t/43_vg_simplify.t: line 24: vg: command not found t/43_vg_simplify.t: line 24: vg: command not found t/43_vg_simplify.t: line 24: vg: command not found t/43_vg_simplify.t .... 1..5 not ok 1 - vg simplify runs through when popping small bubbles # got: '127' # expected: '0' not ok 2 - simplification pops all the bubbles in a simple graph # got: '' # expected: '1' not ok 3 - vg simplify runs through when removing rare variants # got: '127' # expected: '0' not ok 4 - the graph is valid after removing rare variants # got: '127' # expected: '0' not ok 5 - simplification keeps only some variants # got: '' # expected: '118' Failed 5/5 subtests t/44_vg_benchmark.t: line 10: vg: command not found t/44_vg_benchmark.t ... 1..1 not ok 1 - vg benchmark completes succesfully # got: '127' # expected: '0' Failed 1/1 subtests t/45_vg_sort.t: line 12: vg: command not found t/45_vg_sort.t: line 12: vg: command not found t/45_vg_sort.t: line 14: vg: command not found t/45_vg_sort.t: line 21: vg: command not found t/45_vg_sort.t: line 25: vg: command not found t/45_vg_sort.t: line 28: vg: command not found t/45_vg_sort.t: line 31: vg: command not found t/45_vg_sort.t ........ 1..5 not ok 1 - ids in our test graph are not initially in sorted order # got: '0' # expected: '1' not ok 2 - a vg graph can be sorted and indexed by ID without crashing # got: '127' # expected: '0' not ok 3 - a vg graph can be sorted topologically # got: '127' # expected: '0' not ok 4 - a vg graph can be sorted with Eades algorithm without crashing # got: '127' # expected: '0' not ok 5 - a vg graph can be sorted with the max-flow algorithm without crashing # got: '127' # expected: '0' Failed 5/5 subtests t/46_vg_minimizer.t: line 13: vg: command not found t/46_vg_minimizer.t: line 14: vg: command not found t/46_vg_minimizer.t: line 15: vg: command not found t/46_vg_minimizer.t: line 18: vg: command not found t/46_vg_minimizer.t: line 26: vg: command not found md5sum: x.mi: No such file or directory t/46_vg_minimizer.t: line 31: vg: command not found md5sum: x.mi: No such file or directory t/46_vg_minimizer.t: line 36: vg: command not found md5sum: x.mi: No such file or directory t/46_vg_minimizer.t: line 41: vg: command not found t/46_vg_minimizer.t: line 42: vg: command not found md5sum: x.mi: No such file or directory t/46_vg_minimizer.t: line 47: vg: command not found t/46_vg_minimizer.t: line 48: vg: command not found md5sum: x.mi: No such file or directory t/46_vg_minimizer.t: line 53: vg: command not found t/46_vg_minimizer.t: line 64: vg: command not found t/46_vg_minimizer.t: line 65: vg: command not found t/46_vg_minimizer.t: line 66: vg: command not found t/46_vg_minimizer.t: line 69: vg: command not found t/46_vg_minimizer.t: line 71: vg: command not found md5sum: xy.mi: No such file or directory t/46_vg_minimizer.t ... 1..16 not ok 1 - default parameters # got: '127' # expected: '0' not ok 2 - distance index or --no-dist is required # got: '127' # expected: '1' not ok 3 - single-threaded construction # got: '127' # expected: '0' not ok 4 - unnamed test # got: '0d75343d78d1e7d9e9fbc3d7d2386ce2' # expected: 'construction is deterministic' not ok 5 - syncmer index # got: '127' # expected: '0' not ok 6 - unnamed test # got: '74d836b46799590835c7d61e283df4f0' # expected: 'construction is deterministic' not ok 7 - minimizer parameters # got: '127' # expected: '0' not ok 8 - unnamed test # got: '7260e5ea22f063a8dff1f9dd60f92288' # expected: 'setting -k -w works correctly' not ok 9 - construction from GBWTGraph # got: '127' # expected: '0' not ok 10 - unnamed test # got: '0d75343d78d1e7d9e9fbc3d7d2386ce2' # expected: 'construction is deterministic' not ok 11 - construction from GBZ # got: '127' # expected: '0' not ok 12 - unnamed test # got: '0d75343d78d1e7d9e9fbc3d7d2386ce2' # expected: 'construction is deterministic' not ok 13 - construction with payload # got: '127' # expected: '0' not ok 14 - multiple graphs: first # got: '127' # expected: '0' not ok 15 - multiple graphs: second # got: '127' # expected: '0' not ok 16 - unnamed test # got: '1ca39921b15cc3e7d27919a3ec7f47fa' # expected: 'construction is deterministic' Failed 16/16 subtests t/47_vg_dotplot.t: line 10: vg: command not found t/47_vg_dotplot.t: line 11: vg: command not found t/47_vg_dotplot.t: line 12: vg: command not found t/47_vg_dotplot.t ..... 1..1 not ok 1 - vg dotplot runs successfully # got: '127' # expected: '0' Failed 1/1 subtests t/48_vg_convert.t: line 12: vg: command not found t/48_vg_convert.t: line 13: vg: command not found t/48_vg_convert.t: line 13: vg: command not found t/48_vg_convert.t: line 13: vg: command not found t/48_vg_convert.t: line 15: vg: command not found t/48_vg_convert.t: line 16: vg: command not found t/48_vg_convert.t: line 17: vg: command not found t/48_vg_convert.t: line 17: vg: command not found t/48_vg_convert.t: line 17: vg: command not found t/48_vg_convert.t: line 23: vg: command not found t/48_vg_convert.t: line 24: vg: command not found t/48_vg_convert.t: line 25: vg: command not found t/48_vg_convert.t: line 25: vg: command not found t/48_vg_convert.t: line 25: vg: command not found t/48_vg_convert.t: line 31: vg: command not found t/48_vg_convert.t: line 32: vg: command not found t/48_vg_convert.t: line 33: vg: command not found t/48_vg_convert.t: line 33: vg: command not found t/48_vg_convert.t: line 33: vg: command not found t/48_vg_convert.t: line 39: vg: command not found t/48_vg_convert.t: line 40: vg: command not found t/48_vg_convert.t: line 41: vg: command not found t/48_vg_convert.t: line 41: vg: command not found t/48_vg_convert.t: line 41: vg: command not found t/48_vg_convert.t: line 48: vg: command not found t/48_vg_convert.t: line 49: vg: command not found t/48_vg_convert.t: line 51: vg: command not found t/48_vg_convert.t: line 51: vg: command not found t/48_vg_convert.t: line 52: vg: command not found t/48_vg_convert.t: line 52: vg: command not found t/48_vg_convert.t: line 53: vg: command not found t/48_vg_convert.t: line 53: vg: command not found t/48_vg_convert.t: line 54: vg: command not found t/48_vg_convert.t: line 54: vg: command not found t/48_vg_convert.t: line 54: vg: command not found t/48_vg_convert.t: line 55: vg: command not found t/48_vg_convert.t: line 55: vg: command not found t/48_vg_convert.t: line 55: vg: command not found t/48_vg_convert.t: line 57: vg: command not found t/48_vg_convert.t: line 57: vg: command not found t/48_vg_convert.t: line 58: vg: command not found t/48_vg_convert.t: line 58: vg: command not found t/48_vg_convert.t: line 59: vg: command not found t/48_vg_convert.t: line 59: vg: command not found t/48_vg_convert.t: line 59: vg: command not found t/48_vg_convert.t: line 60: vg: command not found t/48_vg_convert.t: line 60: vg: command not found t/48_vg_convert.t: line 60: vg: command not found t/48_vg_convert.t: line 60: vg: command not found t/48_vg_convert.t: line 65: vg: command not found t/48_vg_convert.t: line 66: vg: command not found t/48_vg_convert.t: line 67: vg: command not found t/48_vg_convert.t: line 68: vg: command not found t/48_vg_convert.t: line 69: vg: command not found t/48_vg_convert.t: line 70: vg: command not found t/48_vg_convert.t: line 70: vg: command not found t/48_vg_convert.t: line 74: vg: command not found t/48_vg_convert.t: line 74: vg: command not found t/48_vg_convert.t: line 74: vg: command not found t/48_vg_convert.t: line 79: vg: command not found t/48_vg_convert.t: line 79: vg: command not found t/48_vg_convert.t: line 79: vg: command not found t/48_vg_convert.t: line 84: vg: command not found t/48_vg_convert.t: line 86: vg: command not found t/48_vg_convert.t: line 88: vg: command not found t/48_vg_convert.t: line 89: vg: command not found t/48_vg_convert.t: line 90: vg: command not found t/48_vg_convert.t: line 91: vg: command not found t/48_vg_convert.t: line 95: vg: command not found t/48_vg_convert.t: line 96: vg: command not found t/48_vg_convert.t: line 100: vg: command not found t/48_vg_convert.t: line 111: vg: command not found t/48_vg_convert.t: line 111: vg: command not found t/48_vg_convert.t: line 119: vg: command not found t/48_vg_convert.t: line 120: vg: command not found t/48_vg_convert.t: line 121: vg: command not found t/48_vg_convert.t: line 122: vg: command not found t/48_vg_convert.t: line 123: vg: command not found t/48_vg_convert.t: line 124: vg: command not found t/48_vg_convert.t: line 125: vg: command not found t/48_vg_convert.t: line 126: vg: command not found t/48_vg_convert.t: line 130: vg: command not found t/48_vg_convert.t: line 135: vg: command not found t/48_vg_convert.t: line 136: vg: command not found t/48_vg_convert.t: line 138: vg: command not found t/48_vg_convert.t: line 138: vg: command not found t/48_vg_convert.t: line 156: vg: command not found t/48_vg_convert.t: line 157: vg: command not found t/48_vg_convert.t: line 158: vg: command not found t/48_vg_convert.t: line 159: vg: command not found t/48_vg_convert.t: line 160: vg: command not found t/48_vg_convert.t: line 160: vg: command not found t/48_vg_convert.t: line 164: vg: command not found t/48_vg_convert.t: line 164: vg: command not found t/48_vg_convert.t: line 171: vg: command not found t/48_vg_convert.t: line 172: vg: command not found t/48_vg_convert.t: line 173: vg: command not found t/48_vg_convert.t: line 174: vg: command not found t/48_vg_convert.t: line 175: vg: command not found t/48_vg_convert.t: line 175: vg: command not found t/48_vg_convert.t: line 179: vg: command not found t/48_vg_convert.t: line 179: vg: command not found t/48_vg_convert.t: line 185: vg: command not found t/48_vg_convert.t: line 185: vg: command not found t/48_vg_convert.t: line 186: vg: command not found t/48_vg_convert.t: line 186: vg: command not found t/48_vg_convert.t: line 192: vg: command not found t/48_vg_convert.t: line 192: vg: command not found t/48_vg_convert.t: line 194: vg: command not found awk: fatal: cannot open file `gfa-id-mapping.tsv' for reading: No such file or directory awk: fatal: cannot open file `gfa-id-mapping.tsv' for reading: No such file or directory t/48_vg_convert.t: line 206: vg: command not found t/48_vg_convert.t: line 206: vg: command not found t/48_vg_convert.t: line 208: vg: command not found t/48_vg_convert.t: line 208: vg: command not found t/48_vg_convert.t: line 209: vg: command not found t/48_vg_convert.t: line 220: vg: command not found t/48_vg_convert.t: line 225: vg: command not found cmp: EOF on converted.gfa which is empty t/48_vg_convert.t: line 229: vg: command not found cmp: EOF on converted.gfa which is empty t/48_vg_convert.t: line 234: vg: command not found t/48_vg_convert.t: line 238: vg: command not found cmp: EOF on converted.gfa which is empty t/48_vg_convert.t: line 243: vg: command not found cmp: EOF on extracted.gfa which is empty t/48_vg_convert.t: line 247: vg: command not found cmp: EOF on extracted.gfa which is empty t/48_vg_convert.t: line 253: vg: command not found cmp: EOF on extracted.gfa which is empty t/48_vg_convert.t: line 263: vg: command not found t/48_vg_convert.t: line 266: vg: command not found cmp: EOF on converted.gfa which is empty t/48_vg_convert.t: line 276: vg: command not found t/48_vg_convert.t: line 277: vg: command not found t/48_vg_convert.t: line 278: vg: command not found t/48_vg_convert.t: line 279: vg: command not found t/48_vg_convert.t: line 280: vg: command not found t/48_vg_convert.t: line 284: vg: command not found t/48_vg_convert.t: line 286: vg: command not found t/48_vg_convert.t: line 289: vg: command not found t/48_vg_convert.t: line 294: vg: command not found t/48_vg_convert.t: line 296: vg: command not found t/48_vg_convert.t: line 299: vg: command not found t/48_vg_convert.t: line 304: vg: command not found t/48_vg_convert.t: line 306: vg: command not found t/48_vg_convert.t: line 309: vg: command not found t/48_vg_convert.t: line 314: vg: command not found t/48_vg_convert.t: line 316: vg: command not found t/48_vg_convert.t: line 319: vg: command not found t/48_vg_convert.t: line 324: vg: command not found t/48_vg_convert.t: line 326: vg: command not found t/48_vg_convert.t: line 327: vg: command not found t/48_vg_convert.t: line 329: vg: command not found t/48_vg_convert.t: line 332: vg: command not found cmp: EOF on extracted.gfa which is empty t/48_vg_convert.t: line 336: vg: command not found cmp: EOF on extracted.gfa which is empty t/48_vg_convert.t: line 342: vg: command not found t/48_vg_convert.t: line 344: vg: command not found cmp: EOF on extracted.gfa which is empty t/48_vg_convert.t: line 348: vg: command not found t/48_vg_convert.t: line 354: vg: command not found cmp: EOF on gbz.gfa which is empty t/48_vg_convert.t: line 360: vg: command not found cmp: EOF on sorted.gfa which is empty t/48_vg_convert.t: line 365: vg: command not found t/48_vg_convert.t: line 366: vg: command not found t/48_vg_convert.t: line 369: vg: command not found t/48_vg_convert.t: line 387: vg: command not found t/48_vg_convert.t: line 388: vg: command not found t/48_vg_convert.t: line 389: vg: command not found t/48_vg_convert.t: line 392: vg: command not found t/48_vg_convert.t: line 393: vg: command not found t/48_vg_convert.t: line 396: vg: command not found t/48_vg_convert.t: line 397: vg: command not found t/48_vg_convert.t: line 400: vg: command not found t/48_vg_convert.t: line 401: vg: command not found t/48_vg_convert.t: line 407: vg: command not found t/48_vg_convert.t: line 408: vg: command not found t/48_vg_convert.t: line 409: vg: command not found t/48_vg_convert.t: line 410: vg: command not found t/48_vg_convert.t: line 413: vg: command not found t/48_vg_convert.t: line 414: vg: command not found t/48_vg_convert.t: line 420: vg: command not found t/48_vg_convert.t: line 422: vg: command not found t/48_vg_convert.t: line 425: vg: command not found t/48_vg_convert.t: line 427: vg: command not found t/48_vg_convert.t: line 436: vg: command not found t/48_vg_convert.t: line 436: vg: command not found t/48_vg_convert.t: line 437: vg: command not found t/48_vg_convert.t: line 437: vg: command not found t/48_vg_convert.t: line 443: vg: command not found t/48_vg_convert.t: line 449: vg: command not found t/48_vg_convert.t: line 455: vg: command not found t/48_vg_convert.t: line 455: vg: command not found t/48_vg_convert.t: line 455: vg: command not found t/48_vg_convert.t: line 455: vg: command not found t/48_vg_convert.t: line 456: vg: command not found t/48_vg_convert.t: line 456: vg: command not found t/48_vg_convert.t: line 459: vg: command not found t/48_vg_convert.t: line 459: vg: command not found t/48_vg_convert.t: line 462: vg: command not found t/48_vg_convert.t: line 467: vg: command not found t/48_vg_convert.t: line 479: vg: command not found t/48_vg_convert.t: line 480: vg: command not found t/48_vg_convert.t: line 488: vg: command not found t/48_vg_convert.t: line 489: vg: command not found t/48_vg_convert.t: line 490: vg: command not found t/48_vg_convert.t: line 491: vg: command not found t/48_vg_convert.t: line 492: vg: command not found t/48_vg_convert.t: line 493: vg: command not found t/48_vg_convert.t: line 496: vg: command not found t/48_vg_convert.t: line 501: vg: command not found t/48_vg_convert.t: line 502: vg: command not found t/48_vg_convert.t: line 503: vg: command not found t/48_vg_convert.t: line 504: vg: command not found t/48_vg_convert.t: line 505: vg: command not found t/48_vg_convert.t: line 506: vg: command not found t/48_vg_convert.t: line 507: vg: command not found t/48_vg_convert.t: line 510: vg: command not found t/48_vg_convert.t ..... 1..106 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 gfa conversion ok 5 - hash graph conversion looks good ok 6 - packed graph conversion looks good ok 7 - vg conversion looks good ok 8 - gfa 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 - gfa to gfa conversion looks good ok 14 - vg convert gam -> gaf -> gam -> gaf makes same gaf twice ok 15 - vg convert gam -> gaf -> gam -> gaf gives same result multithreaded as with -t 1 ok 16 - vg convert gam -> gaf.gz -> gam -> gaf gives same result multithreaded as with -t 1 ok 17 - vg convert gam -> gaf -> gam produces same gam Paths with snps and indels ok 18 - vg convert gam -> gaf -> gam preserves sequence ok 19 - vg convert gam -> gaf -> gam -> gaf makes same gaf twice in presence of indels and snps 0a1 > * 78 0 78 + >20>21>23>24>26>27>29>30>32>33>35 102 22 102 71 80 60 AS:i:47 cs:Z::13*GN*GN:8+NNN:16*GN*TN:18-ACTAG:16 not ok 20 - vg convert cg-gaf -> gam -> cs-gaf gives expected output (snps converted to matches, insertion converted to Ns) # got: '1' # expected: '0' ok 21 - vg convert gam -> gaf -> gam preserves sequences of 1mb1kgp simulated reads ok 22 - vg convert gam -> gaf -> gam ->gaf makes same gaf each time on 1mb1kgp simulated reads not ok 23 - split alignment converted using deletions to represent internal offsets # got: '' # expected: 'cs:Z::13-CCAGTGCTCGCATC:2' ok 24 - vg convert gam -> gaf ->gam -> gaf makes same gaf each time for split alignment ok 25 - convert gam->gaf->gam on softclipped read preserves sequence ok 26 - convert gam->gaf->gam->gaf makes same gaf each time of soft clipped alignment ok 27 - convert gam->gaf->gam on read with floating insertion preserves sequence ok 28 - convert gam->gaf->gam->gaf makes same gaf each time of floating insertion alignment ok 29 - converting gfa and equivalent rgfa produces same output not ok 30 - rank-1 rgfa subpath found # got: '' # expected: 'y[35]' 1,15d0 < 12 < s1 < s10 < s11 < s13 < s14 < s15 < s2 < s3 < s4 < s5 < s6 < s7 < s8 < s9 not ok 31 - 2nd column of gfa id translation file contains all rgfa nodes # got: '1' # expected: '0' 1,15d0 < 1 < 10 < 11 < 12 < 13 < 14 < 15 < 2 < 3 < 4 < 5 < 6 < 7 < 8 < 9 not ok 32 - 3rd column of gfa id translation file contains all gfa nodes # got: '1' # expected: '0' ok 33 - rgfa output wrote no P-lines ok 34 - rgfa export roundtrips back to normal P-lines not ok 35 - GBWTGraph to HashGraph conversion # got: '127' # expected: '0' not ok 36 - GFA -> GBWTGraph -> HashGraph -> GFA conversion maintains segments # got: '1' # expected: '0' not ok 37 - GFA -> GBWTGraph -> HashGraph -> GFA conversion maintains walks # got: '1' # expected: '0' not ok 38 - GBZ to HashGraph conversion # got: '127' # expected: '0' not ok 39 - GFA -> GBZ -> HashGraph -> GFA conversion maintains segments # got: '1' # expected: '0' not ok 40 - GBWTGraph to GFA conversion with walks, GBWTGraph algorithm # got: '127' # expected: '0' not ok 41 - GBWTGraph to GFA conversion with GBWTGraph algorithm creates the correct normalized GFA file # got: '1' # expected: '0' ok 42 - GBWTGraph to GFA conversion with walks, vg algorithm not ok 43 - GBWTGraph to GFA conversion with vg algorithm creates the correct possibly-unnormalized GFA file # got: '1' # expected: '0' not ok 44 - GBZ to GFA conversion with walks, GBWTGraph algorithm # got: '127' # expected: '0' not ok 45 - GBZ to GFA conversion with GBWTGraph algorithm creates the correct normalized GFA file # got: '1' # expected: '0' not ok 46 - GFA to HashGraph conversion # got: '127' # expected: '0' not ok 47 - GFA -> HashGraph -> GFA conversion maintains segments, links, walks, and paths # got: '1' # expected: '0' not ok 48 - GBWTGraph to HashGraph conversion with generic paths # got: '127' # expected: '0' ok 49 - GBWTGraph to HashGraph conversion creates the correct generic paths ok 50 - GBWTGraph to HashGraph conversion creates the correct haplotype paths not ok 51 - GBZ to HashGraph conversion with generic paths # got: '127' # expected: '0' ok 52 - GBZ to HashGraph conversion creates the correct generic paths ok 53 - GBZ to HashGraph conversion creates the correct haplotype paths not ok 54 - GBWTGraph to XG conversion with generic paths # got: '127' # expected: '0' ok 55 - GBWTGraph to XG conversion creates the correct generic paths ok 56 - GBWTGraph to XG conversion creates the correct haplotype paths not ok 57 - GBZ to XG conversion with generic paths # got: '127' # expected: '0' ok 58 - GBZ to XG conversion creates the correct generic paths ok 59 - GBZ to XG conversion creates the correct haplotype paths not ok 60 - GBZ to XG conversion while dropping haplotypes # got: '127' # expected: '0' not ok 61 - No haplotypes in the converted graph # got: '0' # expected: '2' not ok 62 - GBZ to HashGraph conversion while dropping haplotypes # got: '127' # expected: '0' not ok 63 - No haplotypes in the converted graph # got: '0' # expected: '2' not ok 64 - GBWTGraph to GFA conversion with paths and walks, GBWTGraph algorithm # got: '127' # expected: '0' not ok 65 - GBWTGraph to GFA conversion with GBWTGraph algorithm creates the expected normalized GFA file # got: '1' # expected: '0' ok 66 - GBWTGraph to GFA conversion with paths and walks, vg algorithm not ok 67 - GBWTGraph to GFA conversion with vg algorithm creates the correct possibly-unnormalized GFA file # got: '1' # expected: '0' not ok 68 - GBWTGraph to HashGraph conversion with paths and walks # got: '127' # expected: '0' ok 69 - HashGraph to GFA conversion with paths and walks not ok 70 - GBWTGraph to HashGraph to GFA conversion creates the correct possibly-unnormalized GFA file # got: '1' # expected: '0' not ok 71 - HashGraph to GFA conversion writing walks as paths # got: '127' # expected: '0' ok 72 - HashGraph to GFA conversion writing walks as paths produces no walks not ok 73 - HashGraph to GFA conversion writing walks as paths produces all expected paths # got: '0' # expected: '6' not ok 74 - GBZ to GFA conversion with paths and walks, GBWTGraph algorithm # got: '127' # expected: '0' not ok 75 - GBZ to GFA conversion with GBWTGraph algorithm creates the correct normalized GFA file # got: '1' # expected: '0' not ok 76 - GBZ to GFA conversion works with multiple threads # got: '1' # expected: '0' not ok 77 - GBZ to GFA with translation # got: '127' # expected: '0' not ok 78 - 8 segments # got: '0' # expected: '8' not ok 79 - GBZ to GFA without translation # got: '127' # expected: '0' not ok 80 - 9 segments # got: '0' # expected: '9' ok 81 - GFA -> GBZ conversion preserves path metadata ok 82 - GFA -> GBZ -> GFA conversion preserves path metadata ok 83 - GFA -> HashGraph conversion preserves path metadata ok 84 - GFA -> HashGraph -> GFA conversion preserves path metadata ok 85 - rGFA -> HashGraph -> GBZ conversion preserves path metadata ok 86 - rGFA -> HashGraph -> GBZ -> GFA conversion preserves path metadata not ok 87 - GFA -> HashGraph conversion works with redundant paths # got: '127' # expected: '0' not ok 88 - GFA -> HashGraph conversion with redundant paths keeps one copy of the redundant path # got: '0' # expected: '1' not ok 89 - GFA -> HashGraph conversion works with two-part reference path names # got: '127' # expected: '0' not ok 90 - GFA -> HashGraph conversion with with two-part reference path names gets the right paths # got: '0' # expected: '2' ok 91 - No difference roundtripping a GFA if it's loaded as a GFA or HandleGraph t/48_vg_convert.t: line 443: vg: command not found ok 92 - Streaming an unsorted GFA gives same output as sorted not ok 93 - Warning given when falling back to temp GFA buffer file # got: '0' # expected: '1' t/48_vg_convert.t: line 449: vg: command not found ok 94 - Streaming an sorted GFA gives same output as reading from file not ok 95 - No warnings given when streamed GFA is sorted # got: '1' # expected: '0' ok 96 - Modding GFA directly produces same output as going through convert ok 97 - Modding sorted GFA stream produces same output as going through convert t/48_vg_convert.t: line 462: vg: command not found ok 98 - Modding unsorted GFA stream produces same output as going through convert not ok 99 - Warning given when falling back to temp GFA buffer file in mod # got: '0' # expected: '1' t/48_vg_convert.t: line 467: vg: command not found ok 100 - Modding unsorted GFA file produces same output as going through convert not ok 101 - No warnings given when input GFA file is unsorted # got: '1' # expected: '0' ok 102 - rGFA handled consistently when streaming as when loaded from file ok 103 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output (GAF check) not ok 104 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output (GAM check) # got: '127' # expected: '0' ok 105 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output for long node (GAF check) not ok 106 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output for long node (GAM check) # got: '127' # expected: '0' Failed 49/106 subtests t/49_vg_depth.t: line 10: vg: command not found t/49_vg_depth.t: line 11: vg: command not found t/49_vg_depth.t: line 11: vg: command not found t/49_vg_depth.t: line 12: vg: command not found t/49_vg_depth.t: line 13: vg: command not found t/49_vg_depth.t: line 14: vg: command not found t/49_vg_depth.t: line 15: vg: command not found t/49_vg_depth.t: line 17: vg: command not found t/49_vg_depth.t: line 18: vg: command not found t/49_vg_depth.t: line 19: vg: command not found t/49_vg_depth.t: line 20: vg: command not found t/49_vg_depth.t: line 21: vg: command not found t/49_vg_depth.t: line 22: vg: command not found t/49_vg_depth.t: line 23: vg: command not found t/49_vg_depth.t: line 23: vg: command not found t/49_vg_depth.t: line 24: vg: command not found t/49_vg_depth.t ....... 1..6 not ok 1 - unnamed test # got: '18' # expected: 'vg depth gets correct depth from gam' not ok 2 - unnamed test # got: '18' # expected: 'vg depth gets correct depth from pack' not ok 3 - vg depth gets correct number of bins # got: '0' # expected: '5' not ok 4 - unnamed test # got: '18' # expected: 'vg depth gets correct depth from gaf' ok 5 - vg depth of paths reports all paths not ok 6 - vg depth of paths reports just path with selected prefix # got: '0' # expected: '1' Failed 5/6 subtests t/50_vg_giraffe.t: line 10: vg: command not found t/50_vg_giraffe.t: line 11: vg: command not found t/50_vg_giraffe.t: line 12: vg: command not found t/50_vg_giraffe.t: line 13: vg: command not found t/50_vg_giraffe.t: line 14: vg: command not found t/50_vg_giraffe.t: line 15: vg: command not found t/50_vg_giraffe.t: line 16: vg: command not found t/50_vg_giraffe.t: line 17: vg: command not found t/50_vg_giraffe.t: line 19: vg: command not found t/50_vg_giraffe.t: line 23: vg: command not found t/50_vg_giraffe.t: line 27: vg: command not found t/50_vg_giraffe.t: line 28: vg: command not found t/50_vg_giraffe.t: line 32: vg: command not found t/50_vg_giraffe.t: line 35: vg: command not found t/50_vg_giraffe.t: line 38: vg: command not found t/50_vg_giraffe.t: line 40: vg: command not found t/50_vg_giraffe.t: line 42: vg: command not found t/50_vg_giraffe.t: line 45: vg: command not found t/50_vg_giraffe.t: line 48: vg: command not found t/50_vg_giraffe.t: line 49: vg: command not found t/50_vg_giraffe.t: line 52: vg: command not found t/50_vg_giraffe.t: line 54: vg: command not found chmod: cannot access 'x.dist': No such file or directory t/50_vg_giraffe.t: line 58: vg: command not found t/50_vg_giraffe.t: line 66: vg: command not found t/50_vg_giraffe.t: line 67: vg: command not found t/50_vg_giraffe.t: line 79: vg: command not found t/50_vg_giraffe.t: line 85: vg: command not found t/50_vg_giraffe.t: line 86: vg: command not found t/50_vg_giraffe.t: line 87: vg: command not found t/50_vg_giraffe.t: line 104: vg: command not found t/50_vg_giraffe.t: line 105: vg: command not found t/50_vg_giraffe.t: line 107: vg: command not found t/50_vg_giraffe.t: line 108: vg: command not found t/50_vg_giraffe.t: line 111: vg: command not found t/50_vg_giraffe.t: line 111: vg: command not found t/50_vg_giraffe.t: line 111: vg: command not found t/50_vg_giraffe.t: line 119: vg: command not found t/50_vg_giraffe.t: line 119: vg: command not found t/50_vg_giraffe.t: line 119: vg: command not found t/50_vg_giraffe.t: line 133: vg: command not found t/50_vg_giraffe.t: line 134: vg: command not found t/50_vg_giraffe.t: line 144: vg: command not found t/50_vg_giraffe.t: line 145: vg: command not found t/50_vg_giraffe.t: line 147: vg: command not found t/50_vg_giraffe.t: line 156: vg: command not found t/50_vg_giraffe.t: line 165: vg: command not found t/50_vg_giraffe.t: line 168: vg: command not found t/50_vg_giraffe.t: line 173: vg: command not found t/50_vg_giraffe.t: line 176: vg: command not found t/50_vg_giraffe.t: line 185: vg: command not found [main_samview] fail to read the header from "xy.bam". t/50_vg_giraffe.t: line 192: vg: command not found t/50_vg_giraffe.t: line 193: vg: command not found t/50_vg_giraffe.t: line 194: vg: command not found t/50_vg_giraffe.t: line 196: vg: command not found t/50_vg_giraffe.t: line 197: vg: command not found t/50_vg_giraffe.t: line 199: vg: command not found t/50_vg_giraffe.t: line 202: vg: command not found t/50_vg_giraffe.t: line 211: vg: command not found t/50_vg_giraffe.t: line 212: vg: command not found t/50_vg_giraffe.t: line 213: vg: command not found t/50_vg_giraffe.t: line 215: vg: command not found t/50_vg_giraffe.t: line 216: vg: command not found t/50_vg_giraffe.t: line 217: vg: command not found t/50_vg_giraffe.t ..... 1..50 not ok 1 - a read can be mapped with xg + gbwt + min + dist specified without crashing # got: '127' # expected: '0' not ok 2 - a read can be mapped with gbz + min + dist specified without crashing # got: '127' # expected: '0' not ok 3 - a read can be mapped with gg + gbwt + min + dist specified without crashing # got: '127' # expected: '0' not ok 4 - a read can be mapped with the minimizer index being regenerated # got: '127' # expected: '0' not ok 5 - a read can be mapped with the indexes being inferred by name # got: '127' # expected: '0' not ok 6 - Mapping logs runtime per read # got: '0' # expected: '1' not ok 7 - Mapping produces the correct score # got: '' # expected: '73' not ok 8 - a read can be mapped with the fast preset # got: '127' # expected: '0' not ok 9 - a read can be mapped with the default preset # got: '127' # expected: '0' not ok 10 - Mapping without a full length bonus produces the correct score # got: '' # expected: '63' not ok 11 - a read can be mapped with syncmer indexes without crashing # got: '127' # expected: '0' not ok 12 - a read can be mapped when the distance index is not writable # got: '127' # expected: '0' ok 13 - a read which softclips does not appear to loop not ok 14 - a read can be mapped with just FASTA and VCF without crashing # got: '127' # expected: '0' not ok 15 - mapping with just a FASTA and a VCF produced JSON-able alignments # got: '1' # expected: '0' ok 16 - mapping to manually-generated indexes and automatically-generated indexes is the same ok 17 - mapping with syncmers produces the same alignment as mapping with minimizers not ok 18 - unpaired reads lack cross-references # got: '0' # expected: '1000' ok 19 - paired reads have cross-references 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: '163 # 83' not ok 25 - surjection of unpaired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 26 - surjection of unpaired reads to SAM yields correct pair partner positions # got: '' # expected: '0 # 0' not ok 27 - surjection of unpaired reads to SAM yields distinct QNAMEs # got: '0' # expected: '2' not ok 28 - surjection of unpaired reads to SAM produces absent partner contigs # got: '' # expected: '* # *' not ok 29 - surjection of unpaired reads to SAM produces correct flags # got: '' # expected: '0 # 16' 0a1,3 > @HD VN:1.5 SO:unknown > @SQ SN:y LN:1001 > @SQ SN:x LN:1001 not ok 30 - surjecting with a sequence dictionary in non-sorted order produces headers in non-sorted order # got: '1' # expected: '0' 0a1,3 > @HD VN:1.5 SO:unknown > @SQ SN:x LN:1001 > @SQ SN:y LN:1001 not ok 31 - surjecting with a sequence dictionary in sorted order produces headers in sorted order # got: '1' # expected: '0' not ok 32 - paired reads are evenly split between equivalent mappings # got: '0' # expected: '1' not ok 33 - unpaired reads are evenly split between equivalent mappings # got: '0' # expected: '1' not ok 34 - provenance tracking succeeds for unpaired reads # got: '127' # expected: '0' not ok 35 - correctness tracking succeeds for unpaired reads # got: '127' # expected: '0' not ok 36 - unpaired reads are annotated with minimizer coverage # got: '0' # expected: '2000' not ok 37 - provenance tracking succeeds for paired reads # got: '127' # expected: '0' not ok 38 - correctness tracking succeeds for paired reads # got: '127' # expected: '0' not ok 39 - paired reads are annotated with minimizer coverage # got: '0' # expected: '2000' not ok 40 - paired reads all have nonzero correct minimizer coverage # got: '0' # expected: '2000' not ok 41 - vg giraffe can map to BAM using a GBZ alone # got: '127' # expected: '0' not ok 42 - GBZ-based BAM contains the expected number of reads # got: '0' # expected: '2000' not ok 43 - Mapping reads to named coordinates on a nontrivial graph without walks succeeds # got: '127' # expected: '0' not ok 44 - Reads are all mapped # got: '0' # expected: '200' ok 45 - GFA segment names are all set not ok 46 - Mapping reads as GAF to named coordinates on a nontrivial graph without walks succeeds # got: '127' # expected: '0' ok 47 - Mapping reads as named GAF uses the same names as named GAM not ok 48 - A long read can be correctly aligned # got: '' # expected: '7999' not ok 49 - A long read has the correct edits found # got: '0' # expected: '2' not ok 50 - Long read minimizer set is correctly restricted # got: '0' # expected: '1' Failed 44/50 subtests t/51_vg_combine.t: line 10: vg: command not found t/51_vg_combine.t: line 11: vg: command not found t/51_vg_combine.t: line 11: vg: command not found t/51_vg_combine.t: line 12: vg: command not found t/51_vg_combine.t: line 12: vg: command not found t/51_vg_combine.t: line 14: vg: command not found t/51_vg_combine.t: line 16: vg: command not found t/51_vg_combine.t: line 17: vg: command not found t/51_vg_combine.t: line 18: vg: command not found t/51_vg_combine.t: line 19: vg: command not found t/51_vg_combine.t: line 25: vg: command not found t/51_vg_combine.t: line 25: vg: command not found t/51_vg_combine.t: line 26: vg: command not found t/51_vg_combine.t: line 26: vg: command not found t/51_vg_combine.t: line 26: vg: command not found t/51_vg_combine.t: line 27: vg: command not found t/51_vg_combine.t: line 27: vg: command not found t/51_vg_combine.t: line 27: vg: command not found t/51_vg_combine.t: line 29: vg: command not found t/51_vg_combine.t: line 31: vg: command not found t/51_vg_combine.t: line 32: vg: command not found t/51_vg_combine.t: line 33: vg: command not found t/51_vg_combine.t: line 34: vg: command not found t/51_vg_combine.t: line 40: vg: command not found t/51_vg_combine.t: line 40: vg: command not found t/51_vg_combine.t: line 41: vg: command not found t/51_vg_combine.t: line 41: vg: command not found t/51_vg_combine.t: line 42: vg: command not found t/51_vg_combine.t: line 42: vg: command not found t/51_vg_combine.t: line 44: vg: command not found t/51_vg_combine.t: line 46: vg: command not found t/51_vg_combine.t: line 47: vg: command not found t/51_vg_combine.t: line 48: vg: command not found t/51_vg_combine.t: line 49: vg: command not found t/51_vg_combine.t ..... 1..10 not ok 1 - unnamed test # got: '645' # expected: 'combined graph as correct total nodes' not ok 2 - unnamed test # got: '888' # expected: 'combined graph as correct total edges' ok 3 - combined graph has same input path not ok 4 - unnamed test # got: '645' # expected: 'combined handle graph as correct total nodes' not ok 5 - unnamed test # got: '888' # expected: 'combined handle graph as correct total edges' ok 6 - combined handle graph has same input path not ok 7 - unnamed test # got: '645' # expected: 'path combined graph as correct total nodes' not ok 8 - unnamed test # got: '890' # expected: 'path combined path graph as correct total edges' not ok 9 - path combined graph as correct number of paths # got: '0' # expected: '1' not ok 10 - unnamed test # got: '3003' # expected: 'combined path has correct size' Failed 8/10 subtests rm: cannot remove 'auto.*': No such file or directory t/52_vg_autoindex.t: line 12: vg: command not found ls: cannot access 'auto.*': No such file or directory ls: cannot access 'auto.xg': No such file or directory ls: cannot access 'auto.gcsa*': No such file or directory t/52_vg_autoindex.t: line 17: vg: command not found t/52_vg_autoindex.t: line 17: vg: command not found rm: cannot remove 'auto.*': No such file or directory t/52_vg_autoindex.t: line 22: vg: command not found t/52_vg_autoindex.t: line 24: vg: command not found t/52_vg_autoindex.t: line 24: vg: command not found rm: cannot remove 'auto.*': No such file or directory t/52_vg_autoindex.t: line 29: vg: command not found t/52_vg_autoindex.t: line 31: vg: command not found t/52_vg_autoindex.t: line 31: vg: command not found rm: cannot remove 'auto.*': No such file or directory t/52_vg_autoindex.t: line 36: vg: command not found ls: cannot access 'auto.*': No such file or directory t/52_vg_autoindex.t: line 39: vg: command not found t/52_vg_autoindex.t: line 39: vg: command not found t/52_vg_autoindex.t: line 41: vg: command not found cat: auto.txorigin.tsv: No such file or directory rm: cannot remove 'auto.*': No such file or directory t/52_vg_autoindex.t: line 46: vg: command not found ls: cannot access 'auto.*': No such file or directory t/52_vg_autoindex.t: line 49: vg: command not found t/52_vg_autoindex.t: line 49: vg: command not found rm: cannot remove 'auto.*': No such file or directory t/52_vg_autoindex.t: line 54: vg: command not found ls: cannot access 'auto.*': No such file or directory t/52_vg_autoindex.t: line 57: vg: command not found t/52_vg_autoindex.t: line 57: vg: command not found rm: cannot remove 'auto.*': No such file or directory t/52_vg_autoindex.t: line 62: vg: command not found ls: cannot access 'auto.*': No such file or directory rm: cannot remove 'auto.*': No such file or directory t/52_vg_autoindex.t: line 68: vg: command not found ls: cannot access 'auto.*': No such file or directory t/52_vg_autoindex.t: line 71: vg: command not found t/52_vg_autoindex.t: line 71: vg: command not found rm: cannot remove 'auto.*': No such file or directory t/52_vg_autoindex.t: line 76: vg: command not found rm: cannot remove 'auto.*': No such file or directory t/52_vg_autoindex.t: line 81: vg: command not found rm: cannot remove 'auto.*': No such file or directory t/52_vg_autoindex.t: line 86: vg: command not found t/52_vg_autoindex.t: line 88: vg: command not found t/52_vg_autoindex.t: line 88: vg: command not found rm: cannot remove 'auto.*': No such file or directory t/52_vg_autoindex.t: line 93: vg: command not found t/52_vg_autoindex.t: line 95: vg: command not found t/52_vg_autoindex.t: line 95: vg: command not found rm: cannot remove 'auto.*': No such file or directory t/52_vg_autoindex.t: line 100: vg: command not found rm: cannot remove 'auto.*': No such file or directory t/52_vg_autoindex.t: line 105: vg: command not found rm: cannot remove 'auto.*': No such file or directory t/52_vg_autoindex.t: line 110: vg: command not found ls: cannot access 'auto.*': No such file or directory t/52_vg_autoindex.t: line 113: vg: command not found t/52_vg_autoindex.t: line 114: vg: command not found t/52_vg_autoindex.t: line 115: vg: command not found t/52_vg_autoindex.t: line 115: vg: command not found rm: cannot remove 'auto.*': No such file or directory t/52_vg_autoindex.t: line 121: vg: command not found ls: cannot access 'auto.*': No such file or directory t/52_vg_autoindex.t: line 124: vg: command not found t/52_vg_autoindex.t: line 125: vg: command not found t/52_vg_autoindex.t: line 125: vg: command not found rm: cannot remove 'auto.*': No such file or directory t/52_vg_autoindex.t: line 131: vg: command not found t/52_vg_autoindex.t: line 134: vg: command not found t/52_vg_autoindex.t: line 135: vg: command not found rm: cannot remove 'auto.*': No such file or directory t/52_vg_autoindex.t: line 140: vg: command not found t/52_vg_autoindex.t: line 143: vg: command not found t/52_vg_autoindex.t: line 144: vg: command not found rm: cannot remove 'auto.*': No such file or directory t/52_vg_autoindex.t ... 1..49 not ok 1 - autoindexing successfully completes indexing for vg map with basic input # got: '127' # expected: '0' not ok 2 - autoindexing makes 3 outputs for vg map # got: '0' # expected: '3' not ok 3 - autoindexing makes an XG for vg map # got: '0' # expected: '1' not ok 4 - autoindexing makes a GCSA2/LCP pair for vg map # got: '0' # expected: '2' not ok 5 - basic autoindexing results can be used by vg map # got: '127' # expected: '0' not ok 6 - autoindexing successfully completes indexing for vg map with chunked input # got: '127' # expected: '0' not ok 7 - chunked autoindexing results can be used by vg map # got: '127' # expected: '0' not ok 8 - autoindexing successfully completes indexing for vg map with phased input # got: '127' # expected: '0' not ok 9 - phased autoindexing results can be used by vg map # got: '127' # expected: '0' not ok 10 - autoindexing successfully completes indexing for vg mpmap with unchunked input # got: '127' # expected: '0' not ok 11 - autoindexing creates 6 files for mpmap/rpvg # got: '0' # expected: '6' not ok 12 - basic autoindexing results can be used by vg mpmap # got: '127' # expected: '0' not ok 13 - haplotype transcript GBWT made by autoindex is valid # got: '0' # expected: '6' not ok 14 - transcript origin table has expected number of rows # got: '0' # expected: '7' not ok 15 - autoindexing successfully completes indexing for vg mpmap with unchunked, unphased input # got: '127' # expected: '0' not ok 16 - autoindexing creates 4 files for mpmap/rpvg # got: '0' # expected: '4' not ok 17 - basic unphased autoindexing results can be used by vg mpmap # got: '127' # expected: '0' not ok 18 - autoindexing successfully completes indexing for vg mpmap without variants # got: '127' # expected: '0' not ok 19 - autoindexing creates 4 files for mpmap without variants # got: '0' # expected: '4' not ok 20 - autoindexing results with no variants can be used by vg mpmap # got: '127' # expected: '0' not ok 21 - autoindexing successfully completes indexing for vg mpmap with chunked input # got: '127' # expected: '0' not ok 22 - autoindexing creates 6 files for mpmap/rpvg with chunked input # got: '0' # expected: '6' not ok 23 - autoindexing successfully completes indexing for vg mpmap with unphased chunked input # got: '127' # expected: '0' not ok 24 - autoindexing creates 4 files for mpmap/rpvg with chunked input # got: '0' # expected: '4' not ok 25 - autoindexing results with chunked unphased input can be used by vg mpmap # got: '127' # expected: '0' not ok 26 - autoindexing successfully completes indexing for vg mpmap with partially chunked input # got: '127' # expected: '0' not ok 27 - autoindexing successfully completes indexing for vg mpmap with another partially chunked input # got: '127' # expected: '0' not ok 28 - autoindexing successfully completes indexing for vg mpmap with GFA input # got: '127' # expected: '0' not ok 29 - autoindexing results with GFA input can be used by vg mpmap # got: '127' # expected: '0' not ok 30 - autoindexing successfully completes indexing for vg mpmap with GFA input and a haplotype GTF # got: '127' # expected: '0' not ok 31 - autoindexing results with GFA input and a haplotype GTF can be used by vg mpmap # got: '127' # expected: '0' not ok 32 - autoindexing successfully completes indexing for vg mpmap and rpvg with GFA input # got: '127' # expected: '0' not ok 33 - autoindexing successfully completes indexing for vg mpmap and rpvg with GFA input and a haplotype GTF # got: '127' # expected: '0' not ok 34 - autoindexing successfully completes indexing for vg giraffe with unchunked input # got: '127' # expected: '0' not ok 35 - autoindexing creates 3 inputs for vg giraffe # got: '0' # expected: '3' not ok 36 - basic autoindexing results can be used by vg giraffe # got: '127' # expected: '0' not ok 37 - autoindexing successfully completes indexing for vg giraffe with GFA input with W-lines # got: '127' # expected: '0' not ok 38 - autoindexing creates 3 inputs for vg giraffe from GFA input # got: '0' # expected: '3' not ok 39 - GFA autoindexing results can be used by vg giraffe # got: '127' # expected: '0' not ok 40 - autoindexing successfully completes on a GFA with named segments and W-lines # got: '127' # expected: '0' not ok 41 - GFA segment names are available in output GAM when a walk exists # got: '' # expected: 'Ishmael' not ok 42 - autoindexing successfully completes on a GFA with named segments and no W-lines # got: '127' # expected: '0' not ok 43 - GFA segment names are available in output GAM when no walks exist # got: '' # expected: 'Ishmael' not ok 44 - Running out of room during k-mer enumeration triggers a rewind # got: '0' # expected: '1' ok 45 - Indexing is successful after rewinding from k-mer generation not ok 46 - Running out of room during GCSA2 indexing triggers a rewind # got: '0' # expected: '1' ok 47 - Indexing is successful after rewinding from GCSA2 indexing not ok 48 - Running out of memory during GCSA2 indexing triggers a rewind # got: '0' # expected: '1' ok 49 - Indexing is successful after rewinding from GCSA2 indexing Failed 46/49 subtests t/53_clip.t: line 10: vg: command not found t/53_clip.t: line 10: vg: command not found t/53_clip.t: line 10: vg: command not found t/53_clip.t: line 14: vg: command not found t/53_clip.t: line 15: vg: command not found t/53_clip.t: line 17: vg: command not found t/53_clip.t: line 18: vg: command not found t/53_clip.t: line 21: vg: command not found t/53_clip.t: line 21: vg: command not found t/53_clip.t: line 27: vg: command not found t/53_clip.t: line 28: vg: command not found t/53_clip.t: line 30: vg: command not found t/53_clip.t: line 36: vg: command not found t/53_clip.t: line 37: vg: command not found t/53_clip.t: line 39: vg: command not found t/53_clip.t: line 44: vg: command not found t/53_clip.t: line 45: vg: command not found t/53_clip.t: line 47: vg: command not found t/53_clip.t: line 53: vg: command not found t/53_clip.t: line 54: vg: command not found t/53_clip.t: line 56: vg: command not found t/53_clip.t: line 57: vg: command not found t/53_clip.t: line 65: vg: command not found t/53_clip.t: line 66: vg: command not found t/53_clip.t: line 68: vg: command not found t/53_clip.t: line 74: vg: command not found t/53_clip.t: line 74: vg: command not found t/53_clip.t: line 84: vg: command not found t/53_clip.t: line 89: vg: command not found t/53_clip.t: line 89: vg: command not found t/53_clip.t: line 93: vg: command not found t/53_clip.t: line 93: vg: command not found t/53_clip.t: line 94: vg: command not found t/53_clip.t: line 94: vg: command not found t/53_clip.t ........... 1..17 not ok 1 - clipped graph is valid # got: '127' # expected: '0' ok 2 - every step in clipped graph belongs to reference path not ok 3 - unnamed test # got: 'clipped graph has same length as ref path' # expected: '' not ok 4 - clipped graph is valid # got: '127' # expected: '0' not ok 5 - Just one node filtered # got: '0' # expected: '49' not ok 6 - clipped graph is valid # got: '127' # expected: '0' not ok 7 - Just one edge filtered # got: '0' # expected: '65' not ok 8 - clipped graph is valid # got: '127' # expected: '0' not ok 9 - Just one node filtered # got: '0' # expected: '49' not ok 10 - clipped graph is valid # got: '127' # expected: '0' ok 11 - clipping bad region changes nothing not ok 12 - clipped graph is valid # got: '127' # expected: '0' not ok 13 - Just one node filtered # got: '0' # expected: '49' ok 14 - stub clipping removed all stubs not ok 15 - unnamed test # got: '17' # expected: 'region clipping filtered out only 2 / 4 stub nodes' not ok 16 - unnamed test # got: '1' # expected: 'Correct head after path stubbification' not ok 17 - unnamed test # got: '15' # expected: 'Correct tail after path stubbification' Failed 14/17 subtests t/54_vg_haplotypes.t: line 16: vg: command not found t/54_vg_haplotypes.t: line 17: vg: command not found t/54_vg_haplotypes.t: line 20: vg: command not found t/54_vg_haplotypes.t: line 22: vg: command not found t/54_vg_haplotypes.t: line 24: vg: command not found t/54_vg_haplotypes.t: line 25: vg: command not found t/54_vg_haplotypes.t: line 26: vg: command not found t/54_vg_haplotypes.t: line 29: vg: command not found cmp: indirect.gbz: No such file or directory t/54_vg_haplotypes.t: line 35: vg: command not found t/54_vg_haplotypes.t: line 37: vg: command not found t/54_vg_haplotypes.t: line 38: vg: command not found t/54_vg_haplotypes.t: line 39: vg: command not found t/54_vg_haplotypes.t: line 42: vg: command not found t/54_vg_haplotypes.t: line 44: vg: command not found t/54_vg_haplotypes.t: line 45: vg: command not found t/54_vg_haplotypes.t: line 46: vg: command not found t/54_vg_haplotypes.t: line 49: vg: command not found cmp: diploid.gbz: No such file or directory cmp: diploid.gbz: No such file or directory cmp: full.HG003.gbz: No such file or directory rm: cannot remove 'full.gbz': No such file or directory rm: cannot remove 'full.ri': No such file or directory rm: cannot remove 'full.dist': No such file or directory rm: cannot remove 'full.hapl': No such file or directory t/54_vg_haplotypes.t .. 1..21 not ok 1 - generating haplotype information # got: '127' # expected: '0' not ok 2 - sampling from existing haplotype information # got: '127' # expected: '0' not ok 3 - unnamed test # got: '3' # expected: '1 generated + 2 reference samples' not ok 4 - unnamed test # got: '2' # expected: '2 contigs' not ok 5 - unnamed test # got: '6' # expected: '4 generated + 2 reference haplotypes' not ok 6 - sampling the haplotypes directly # got: '127' # expected: '0' not ok 7 - the outputs are identical # got: '2' # expected: '0' not ok 8 - sampling without adding reference # got: '127' # expected: '0' not ok 9 - unnamed test # got: '1' # expected: '1 sample' not ok 10 - unnamed test # got: '2' # expected: '2 contigs' not ok 11 - unnamed test # got: '4' # expected: '4 haplotypes' not ok 12 - diploid sampling # got: '127' # expected: '0' not ok 13 - unnamed test # got: '3' # expected: '1 generated + 2 reference samples' not ok 14 - unnamed test # got: '2' # expected: '2 contigs' not ok 15 - unnamed test # got: '4' # expected: '2 generated + 2 reference haplotypes' not ok 16 - diploid sampling using a preset # got: '127' # expected: '0' not ok 17 - the outputs are identical # got: '2' # expected: '0' not ok 18 - Giraffe integration with a guessed output name # got: '127' # expected: '0' not ok 19 - the sampled graph is identical to a manually sampled one # got: '2' # expected: '0' not ok 20 - Giraffe integration with a specified output name # got: '127' # expected: '0' not ok 21 - the sampled graphs are identical # got: '2' # expected: '0' Failed 21/21 subtests Test Summary Report ------------------- t/00_unittest.t (Wstat: 0 Tests: 1 Failed: 1) Failed test: 1 t/02_vg_construct.t (Wstat: 0 Tests: 30 Failed: 24) Failed tests: 1-7, 9-11, 13, 17-22, 24-30 t/03_vg_view.t (Wstat: 0 Tests: 23 Failed: 16) Failed tests: 1-4, 6, 11-20, 23 t/04_vg_align.t (Wstat: 0 Tests: 20 Failed: 20) Failed tests: 1-20 t/05_vg_find.t (Wstat: 0 Tests: 29 Failed: 25) Failed tests: 1-14, 16-21, 23-24, 26-27, 29 t/06_vg_index.t (Wstat: 0 Tests: 54 Failed: 51) Failed tests: 1-10, 12-16, 18-36, 38-54 t/07_vg_map.t (Wstat: 0 Tests: 55 Failed: 50) Failed tests: 1-14, 17-22, 25-32, 34-55 t/08_vg_ids.t (Wstat: 0 Tests: 10 Failed: 9) Failed tests: 1-5, 7-10 t/09_vg_concat.t (Wstat: 0 Tests: 4 Failed: 2) Failed tests: 2, 4 t/10_vg_stats.t (Wstat: 0 Tests: 21 Failed: 20) Failed tests: 1-8, 10-21 t/11_vg_paths.t (Wstat: 0 Tests: 20 Failed: 17) Failed tests: 1-7, 9-14, 16-19 t/12_vg_kmers.t (Wstat: 0 Tests: 10 Failed: 10) Failed tests: 1-10 t/13_vg_sim.t (Wstat: 0 Tests: 36 Failed: 31) Failed tests: 1-5, 9-13, 15, 17-36 t/14_vg_mod.t (Wstat: 0 Tests: 32 Failed: 25) Failed tests: 2-11, 13-14, 16, 18-21, 24-25, 27-32 t/15_vg_surject.t (Wstat: 256 (exited 1) Tests: 47 Failed: 42) Failed tests: 1-15, 18-20, 22-35, 38-47 Non-zero exit status: 1 t/16_vg_msga.t (Wstat: 0 Tests: 14 Failed: 12) Failed tests: 1-4, 7-14 t/17_vg_augment.t (Wstat: 0 Tests: 39 Failed: 31) Failed tests: 1-19, 22-23, 26-27, 29-30, 32-33, 35-36 38-39 t/18_vg_call.t (Wstat: 0 Tests: 19 Failed: 6) Failed tests: 2, 11, 14-15, 17-18 t/20_vgtordf.t (Wstat: 0 Tests: 6 Failed: 4) Failed tests: 1-2, 5-6 t/21_vg_filter.t (Wstat: 0 Tests: 13 Failed: 5) Failed tests: 1-2, 5, 9, 12 t/25_circularize.t (Wstat: 0 Tests: 2 Failed: 2) Failed tests: 1-2 t/26_deconstruct.t (Wstat: 0 Tests: 37 Failed: 30) Failed tests: 1-4, 6-10, 12-17, 23-37 t/27_vg_genotype.t (Wstat: 0 Tests: 5 Failed: 4) Failed tests: 1-2, 4-5 t/28_translate.t (Wstat: 0 Tests: 2 Failed: 1) Failed test: 2 t/30_vg_chunk.t (Wstat: 0 Tests: 32 Failed: 20) Failed tests: 1-10, 12-18, 20-22 t/31_vg_add.t (Wstat: 0 Tests: 12 Failed: 8) Failed tests: 1-2, 4, 7-8, 10-12 t/32_vg_snarls.t (Wstat: 0 Tests: 19 Failed: 14) Failed tests: 1-5, 9, 11-18 t/33_vg_mpmap.t (Wstat: 256 (exited 1) Tests: 21 Failed: 20) Failed tests: 1-13, 15-21 Non-zero exit status: 1 t/34_vg_pack.t (Wstat: 0 Tests: 20 Failed: 9) Failed tests: 1-4, 10-11, 18-20 t/36_vg_annotate.t (Wstat: 0 Tests: 9 Failed: 7) Failed tests: 1-2, 5-9 t/37_vg_gbwt.t (Wstat: 0 Tests: 159 Failed: 159) Failed tests: 1-159 t/38_vg_prune.t (Wstat: 0 Tests: 21 Failed: 21) Failed tests: 1-21 t/39_vg_inject.t (Wstat: 256 (exited 1) Tests: 14 Failed: 10) Failed tests: 1-9, 13 Non-zero exit status: 1 t/40_vg_gamcompare.t (Wstat: 0 Tests: 7 Failed: 5) Failed tests: 1-4, 7 t/41_vg_viz.t (Wstat: 0 Tests: 4 Failed: 4) Failed tests: 1-4 t/42_vg_gamsort.t (Wstat: 0 Tests: 2 Failed: 1) Failed test: 2 t/43_vg_simplify.t (Wstat: 0 Tests: 5 Failed: 5) Failed tests: 1-5 t/44_vg_benchmark.t (Wstat: 0 Tests: 1 Failed: 1) Failed test: 1 t/45_vg_sort.t (Wstat: 0 Tests: 5 Failed: 5) Failed tests: 1-5 t/46_vg_minimizer.t (Wstat: 0 Tests: 16 Failed: 16) Failed tests: 1-16 t/47_vg_dotplot.t (Wstat: 0 Tests: 1 Failed: 1) Failed test: 1 t/48_vg_convert.t (Wstat: 0 Tests: 106 Failed: 49) Failed tests: 20, 23, 30-32, 35-41, 43-48, 51, 54, 57 60-65, 67-68, 70-71, 73-80, 87-90, 93, 95 99, 101, 104, 106 t/49_vg_depth.t (Wstat: 0 Tests: 6 Failed: 5) Failed tests: 1-4, 6 t/50_vg_giraffe.t (Wstat: 0 Tests: 50 Failed: 44) Failed tests: 1-12, 14-15, 18, 20-44, 46, 48-50 t/51_vg_combine.t (Wstat: 0 Tests: 10 Failed: 8) Failed tests: 1-2, 4-5, 7-10 t/52_vg_autoindex.t (Wstat: 0 Tests: 49 Failed: 46) Failed tests: 1-44, 46, 48 t/53_clip.t (Wstat: 0 Tests: 17 Failed: 14) Failed tests: 1, 3-10, 12-13, 15-17 t/54_vg_haplotypes.t (Wstat: 0 Tests: 21 Failed: 21) Failed tests: 1-21 Files=53, Tests=1138, 15 wallclock secs ( 0.66 usr 0.16 sys + 7.82 cusr 4.13 csys = 12.77 CPU) Result: FAIL make[1]: [debian/rules:76: override_dh_auto_test-arch] Error 1 (ignored) make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' debian/rules override_dh_auto_test-indep make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' echo No arch independent tests No arch independent tests make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' dh_install debian/bin/simd-dispatch /usr/lib/vg/ dh_install bin/vg* usr/lib/vg/ mkdir -p /build/reproducible-path/vg-1.59.0+ds/debian/vg/usr/bin cd /build/reproducible-path/vg-1.59.0+ds/debian/vg/usr/bin \ && for prog in vg ; do \ ln -s ../lib/vg/simd-dispatch ${prog} ; done make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dwz: Too few files for multifile optimization dh_dwz: warning: No dwz multifile created, but not explicitly requested either so ignoring it. dh_dwz: warning: Common issues include no debug information at all (missing -g) and dh_dwz: warning: compressed debug information (#931891). dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: cannot find library libhandlegraph.so needed by debian/vg/usr/lib/vg/vg-avx (ELF format: 'elf64-x86-64' abi: 'ELF:64:l:amd64:0'; RPATH: '') dpkg-shlibdeps: warning: cannot find library libhandlegraph.so needed by debian/vg/usr/lib/vg/vg-ssse3 (ELF format: 'elf64-x86-64' abi: 'ELF:64:l:amd64:0'; RPATH: '') dpkg-shlibdeps: warning: cannot find library libhandlegraph.so needed by debian/vg/usr/lib/vg/vg-sse3 (ELF format: 'elf64-x86-64' abi: 'ELF:64:l:amd64:0'; RPATH: '') dpkg-shlibdeps: warning: cannot find library libhandlegraph.so needed by debian/vg/usr/lib/vg/vg-plain (ELF format: 'elf64-x86-64' abi: 'ELF:64:l:amd64:0'; RPATH: '') dpkg-shlibdeps: warning: cannot find library libhandlegraph.so needed by debian/vg/usr/lib/vg/vg-avx2 (ELF format: 'elf64-x86-64' abi: 'ELF:64:l:amd64:0'; RPATH: '') dpkg-shlibdeps: warning: cannot find library libhandlegraph.so needed by debian/vg/usr/lib/vg/vg-sse4.1 (ELF format: 'elf64-x86-64' abi: 'ELF:64:l:amd64:0'; RPATH: '') dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.2-1), " make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_md5sums dh_builddeb dpkg-deb: building package 'vg-dbgsym' in '../vg-dbgsym_1.59.0+ds-0.1_amd64.deb'. dpkg-deb: building package 'vg' in '../vg_1.59.0+ds-0.1_amd64.deb'. dpkg-deb: building package 'vg-docs' in '../vg-docs_1.59.0+ds-0.1_all.deb'. dpkg-genbuildinfo --build=binary -O../vg_1.59.0+ds-0.1_amd64.buildinfo dpkg-genchanges --build=binary -O../vg_1.59.0+ds-0.1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration 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/2027625 and its subdirectories I: Current time: Sat Dec 27 10:31:42 -12 2025 I: pbuilder-time-stamp: 1766874702 Sun Nov 24 16:08:59 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Sun Nov 24 16:08:59 UTC 2024 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Sun Nov 24 17:44:46 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Sun Nov 24 17:44:47 UTC 2024 I: vg_1.59.0+ds-0.1_amd64.changes: Format: 1.8 Date: Thu, 21 Nov 2024 00:12:52 +0000 Source: vg Binary: vg vg-dbgsym vg-docs Architecture: amd64 all Version: 1.59.0+ds-0.1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Bastian Germann Description: vg - tools for working with genome variation graphs vg-docs - tools for working with genome variation graphs -- docs Closes: 1013061 1043312 1084554 Changes: vg (1.59.0+ds-0.1) unstable; urgency=medium . * Non-maintainer upload . [ Andreas Tille ] * Update lintian override info to new format: + debian/source/lintian-overrides: line 2 + debian/vg.lintian-overrides: line 5, 8-12 * Remove constraints unnecessary since buster (oldstable): + Build-Depends: Replace dependency on transitional package libncurses5-dev with replacement libtinfo6, libncurses-dev. . [ Pierre Gruet ] * Using tags and filenamemangle in d/watch . [ Michael R. Crusoe ] * New upstream version. Closes: #1013061, #1084554 * Added patch to deal with bashim. * debian/rules: unset LD_PRELOAD for qemu build + testing * debian/rules: if the SIMD level is supported by the build CPU as reported by lscpu, then require the tests for that version of the vg binary to pass. * debian/copyright: freshen * Freshen patches * update clean list * Standards-Version: 4.6.2 (routine-update) * Keep vendored copy of libssw until vg updates to a regular release * Refreshed patches, moved some of the crossbuild fixes into earlier patches to reduce churn. * d/patches/series: skip the ssw patches to use the code copy for now. * d/control: new build-dep: libzstd-dev * Force the use of the system package for SIMDe. * Added patch to fix gcc 12+ issues. * d/copyright: exclude the unused benchmarks.js from the vendored copies of atomic_queue * d/control: update names of obsolete packages to their replacements. Closes: #1043312 * Ignore test failures Checksums-Sha1: 4a84f3fe3fedb826329c7392a77a30a647551de8 1060899216 vg-dbgsym_1.59.0+ds-0.1_amd64.deb 10e7c0f96d3b7238bd4d2cbe5eebbc7de89638ab 2098644 vg-docs_1.59.0+ds-0.1_all.deb e129510067d9883dd22350f2f149231734913ebd 16405 vg_1.59.0+ds-0.1_amd64.buildinfo e56ac49527a3ae82358cc98e89bd80a3058368e0 57614084 vg_1.59.0+ds-0.1_amd64.deb Checksums-Sha256: 9fd2e6884d5f6fc988b06542c97215bfff1c351e4d6e3af55ccf5907bbe5ad1e 1060899216 vg-dbgsym_1.59.0+ds-0.1_amd64.deb 76b06860af84c3a826e14eb484651f4cf94c2035099beea9f3c594641a95421c 2098644 vg-docs_1.59.0+ds-0.1_all.deb 229fc843a3bb86590dc7688960329da61dad4a6aadd714abf237547c1cac81c9 16405 vg_1.59.0+ds-0.1_amd64.buildinfo 0acd8b15fba020cbd7f5e77ad07f5297f8545abf130243fd320cfcb91791251b 57614084 vg_1.59.0+ds-0.1_amd64.deb Files: 8c070490240ac7e5970f37a450786240 1060899216 debug optional vg-dbgsym_1.59.0+ds-0.1_amd64.deb 0a9df9f576e24c3759d9db71c3b55190 2098644 doc optional vg-docs_1.59.0+ds-0.1_all.deb e864326956569dafe12c475baae8c747 16405 science optional vg_1.59.0+ds-0.1_amd64.buildinfo c9ef3da2f66ccc323247c2ab4d7ee6e5 57614084 science optional vg_1.59.0+ds-0.1_amd64.deb Sun Nov 24 17:44:50 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_4-38045.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.4o9ZkNWR/vg_1.59.0+ds-0.1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.4o9ZkNWR/vg_1.59.0+ds-0.1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.4o9ZkNWR/vg_1.59.0+ds-0.1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.4o9ZkNWR/b1/vg_1.59.0+ds-0.1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.4o9ZkNWR/b2/vg_1.59.0+ds-0.1_amd64.changes ## close_archive (total time: 0.000s) 0.000s 14 calls diffoscope.comparators.xz.XzContainer 0.000s 7 calls diffoscope.comparators.deb.DebContainer 0.000s 10 calls diffoscope.comparators.tar.TarContainer 0.000s 4 calls diffoscope.comparators.deb.DebTarContainer ## command (total time: 655.634s) 316.372s 99 calls objdump 234.333s 44 calls diff 62.812s 325 calls readelf 30.223s 2 calls objcopy 9.156s 14 calls xz 2.723s 11 calls strings 0.006s 1 call cmp 0.006s 1 call cmp (external) 0.001s 9 calls cmp (internal) ## compare_files (cumulative) (total time: 46270.165s) 7722.696s 1 call abc.DotChangesFile 7722.631s 1 call abc.DebFile 7722.323s 2 calls abc.XzFile 7720.593s 1 call abc.DebDataTarFile 7719.625s 1 call abc.ElfFile 7658.662s 5 calls diffoscope.comparators.elf.ElfCodeSection 3.603s 3 calls diffoscope.comparators.elf.ElfSection 0.028s 1 call abc.TarFile 0.005s 1 call abc.Md5sumsFile ## container_extract (total time: 19.455s) 9.157s 14 calls diffoscope.comparators.xz.XzContainer 5.220s 24 calls diffoscope.comparators.deb.DebTarContainer 5.070s 16 calls diffoscope.comparators.deb.DebContainer 0.008s 12 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 1.822s) 1.822s 67 calls linediff ## has_same_content_as (total time: 0.009s) 0.007s 2 calls abc.DebFile 0.000s 2 calls abc.TextFile 0.000s 2 calls abc.Md5sumsFile 0.000s 1 call abc.DotChangesFile 0.000s 1 call abc.ElfFile 0.000s 1 call abc.DebDataTarFile 0.000s 1 call abc.TarFile 0.000s 2 calls abc.XzFile 0.000s 5 calls diffoscope.comparators.elf.ElfCodeSection 0.000s 3 calls diffoscope.comparators.elf.ElfSection ## main (total time: 7740.869s) 7740.502s 2 calls outputs 0.367s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 14 calls diffoscope.comparators.xz.XzContainer 0.000s 10 calls diffoscope.comparators.tar.TarContainer 0.000s 8 calls diffoscope.comparators.deb.DebContainer 0.000s 4 calls diffoscope.comparators.deb.DebTarContainer ## output (total time: 2.362s) 2.231s 1 call html 0.084s 1 call text 0.047s 1 call json ## recognizes (total time: 32.015s) 15.070s 12 calls diffoscope.comparators.binary.FilesystemFile 9.326s 1250 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 7.521s 640 calls diffoscope.comparators.utils.archive.ArchiveMember 0.097s 270 calls diffoscope.comparators.debian.DebControlMember ## specialize (total time: 0.163s) 0.163s 20 calls specialize Finished with result: success Main processes terminated with: code=exited/status=1 Service runtime: 2h 9min 1.245s CPU time consumed: 2h 10min 6.101s Sun Nov 24 19:57:55 UTC 2024 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Sun Nov 24 19:57:55 UTC 2024 E: vg failed to build reproducibly in unstable on amd64. Sun Nov 24 19:57:58 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Nov 24 19:57:59 UTC 2024 I: Submitting 20K b1/vg_1.59.0+ds-0.1_amd64.buildinfo.asc Sun Nov 24 19:58:20 UTC 2024 I: Submitting 20K b2/vg_1.59.0+ds-0.1_amd64.buildinfo.asc Sun Nov 24 19:58:49 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Nov 24 19:58:49 UTC 2024 I: Done submitting .buildinfo files. Sun Nov 24 19:58:49 UTC 2024 I: Removing signed vg_1.59.0+ds-0.1_amd64.buildinfo.asc files: removed './b1/vg_1.59.0+ds-0.1_amd64.buildinfo.asc' removed './b2/vg_1.59.0+ds-0.1_amd64.buildinfo.asc'