Running as unit: rb-build-amd64_10-27438.service ==================================================================================== Wed Jan 8 11:48:10 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_10) on jenkins, called using "ionos5-amd64 ionos1-amd64" as arguments. Wed Jan 8 11:48:10 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-Y1vrdMlp" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Jan 8 11:48:10 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Wed Jan 8 11:48:10 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-7KXsGG' Wed Jan 8 11:48:11 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Wed Jan 8 11:48:11 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-FMW8TH' ok, let's check if vg is building anywhere yet… ok, vg is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of vg in unstable on amd64 on jenkins now. 1st build will be done on ionos5-amd64.debian.net. 2nd build will be done on ionos1-amd64.debian.net. ============================================================================= Wed Jan 8 11:48:28 UTC 2025 I: starting to build vg/unstable/amd64 on jenkins on '2025-01-08 11:48' Wed Jan 8 11:48:28 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_10/27438/console.log 1736336908 amd64 unstable vg Wed Jan 8 11:48:28 UTC 2025 I: Downloading source for unstable/vg=1.59.0+ds-0.1 --2025-01-08 11:48:28-- 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% 347M=0s 2025-01-08 11:48:28 (347 MB/s) - ‘vg_1.59.0+ds-0.1.dsc’ saved [2839/2839] --2025-01-08 11:48:28-- 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% 347M=0s 2025-01-08 11:48:28 (347 MB/s) - ‘vg_1.59.0+ds-0.1.dsc’ saved [2839/2839] Wed Jan 8 11:48:28 UTC 2025 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----- Wed Jan 8 11:48:28 UTC 2025 I: Checking whether the package is not for us Wed Jan 8 11:48:28 UTC 2025 I: Starting 1st build on remote node ionos5-amd64.debian.net. Wed Jan 8 11:48:28 UTC 2025 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Wed Jan 8 11:48:28 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Wed Jan 8 11:48:28 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-KPaWJC' ==================================================================================== Tue Feb 10 18:11:29 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos5-amd64, called using "1 vg unstable /srv/reproducible-results/rbuild-debian/r-b-build.oaKNW60N 1.59.0+ds-0.1" as arguments. Tue Feb 10 18:11:29 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-pr64cHEE" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Feb 10 18:11:29 UTC 2026 I: Downloading source for unstable/vg=1.59.0+ds-0.1 Reading package lists... NOTICE: 'vg' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/vg.git Please use: git clone https://salsa.debian.org/med-team/vg.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 69.8 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main vg 1.59.0+ds-0.1 (dsc) [2839 B] Get:2 http://deb.debian.org/debian unstable/main vg 1.59.0+ds-0.1 (tar) [69.7 MB] Get:3 http://deb.debian.org/debian unstable/main vg 1.59.0+ds-0.1 (diff) [117 kB] Fetched 69.8 MB in 1s (60.4 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'vg' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/vg.git Please use: git clone https://salsa.debian.org/med-team/vg.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 69.8 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main vg 1.59.0+ds-0.1 (dsc) [2839 B] Get:2 http://deb.debian.org/debian unstable/main vg 1.59.0+ds-0.1 (tar) [69.7 MB] Get:3 http://deb.debian.org/debian unstable/main vg 1.59.0+ds-0.1 (diff) [117 kB] Fetched 69.8 MB in 1s (60.4 MB/s) Download complete and in download only mode ============================================================================= Building vg in unstable on amd64 on ionos5-amd64 now. Date: Tue Feb 10 18:11:31 UTC 2026 Date UTC: Tue Feb 10 18:11:31 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Feb 10 06:11:31 -12 2026 I: pbuilder-time-stamp: 1770747091 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 dpkg-source: warning: cannot verify inline signature for ./vg_1.59.0+ds-0.1.dsc: unsupported subcommand 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/3414070/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='41f08ad8ee80430d9397ef020d85867e' 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='3414070' 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.oaKNW60N/pbuilderrc_tYfy --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.oaKNW60N/b1 --logfile b1/build.log vg_1.59.0+ds-0.1.dsc' SUDO_GID='110' SUDO_UID='105' 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 ionos5-amd64 6.11.10+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1~bpo12+1 (2024-12-19) 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/3414070/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 ... 19848 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} libffi8{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} libgcrypt20{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} libgnutls30t64{a} libgpg-error0{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} libidn2-0{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} libonig5{a} libosp5{a} libp11-kit-dev{a} libp11-kit0{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{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} libpython3.13-minimal{a} libpython3.13-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{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} libunistring5{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} libxxhash-dev{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} python3.13{a} python3.13-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 libgpg-error-l10n 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, 390 newly installed, 0 to remove and 0 not upgraded. Need to get 269 MB of archives. After unpacking 1102 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 flex amd64 2.6.4-8.2+b4 [423 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [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 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0046 [41.1 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libdebuginfod-common all 0.192-4 [23.7 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.1-3 [858 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.1-3 [2202 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.1-1 [27.0 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-4 [256 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.1-3 [1973 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.1-3 [740 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.1-1 [9912 B] Get: 24 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.1-1 [28.0 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.4.0-2 [1422 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20241223 [164 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-4 [200 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-14 [92.1 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-4 [723 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 bc amd64 1.07.1-4 [103 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 bison amd64 2:3.8.2+dfsg-1+b2 [1170 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 bwa amd64 0.7.18-1 [212 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.31.3-1 [2268 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 53 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.19.0-3+b3 [49.5 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.8-2 [1454 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.19+dfsg-1 [187 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.1-1 [351 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.31.3-1 [11.9 MB] Get: 72 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.23 [90.6 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 79 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-4 [1600 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.23 [919 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 docbook all 4.5-11 [126 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libosp5 amd64 1.5.2-15.1 [973 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 opensp amd64 1.5.2-15.1 [448 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 docbook-to-man amd64 1:2.0.0-47 [73.6 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 docbook-xml all 4.5-13 [77.4 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 docbook-xsl all 1.79.2+dfsg-7 [1221 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.6-1+b1 [26.0 MB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libclang-cpp19 amd64 1:19.1.6-1+b1 [13.2 MB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libclang1-19 amd64 1:19.1.6-1+b1 [7614 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libfmt10 amd64 10.1.1+ds1-4 [127 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 doxygen amd64 1.9.8+ds-2+b3 [5011 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libdw1t64 amd64 0.192-4 [255 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libasm1t64 amd64 0.192-4 [28.4 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.11.1-1 [360 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libjson-c5 amd64 0.18+ds-1 [46.0 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libdebuginfod1t64 amd64 0.192-4 [32.4 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 elfutils amd64 0.192-4 [505 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-4+b2 [4908 B] Get: 110 http://deb.debian.org/debian unstable/main amd64 libfastahack0 amd64 1.0.0+dfsg-11+b2 [26.4 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 fastahack amd64 1.0.0+dfsg-11+b2 [12.7 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.44-3 [280 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 native-architecture all 0.2.3 [2108 B] Get: 120 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.82.4-1 [1501 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libgirepository-2.0-0 amd64 2.82.4-1 [139 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 girepository-tools amd64 2.82.4-1 [145 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libann0 amd64 1.1.2+doc-9+b1 [25.1 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libcdt5 amd64 2.42.4-2+b2 [40.5 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libcgraph6 amd64 2.42.4-2+b2 [64.3 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.11.0-1 [1879 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.0-1+b1 [550 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libgav1-1 amd64 0.19.0-3 [350 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 librav1e0.7 amd64 0.7.1-9 [939 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1899.20250103-1 [173 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.1.1-1 [117 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-dav1d amd64 1.19.5-1 [11.2 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libde265-0 amd64 1.0.15-1+b2 [189 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-libde265 amd64 1.19.5-1 [15.2 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libheif1 amd64 1.19.5-1 [514 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.1.0-2 [478 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b3 [56.2 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libgd3 amd64 2.3.3-12+b1 [126 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libgts-0.7-5t64 amd64 0.7.6+darcs121130-5.2+b1 [160 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b3 [27.8 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.5.4-2 [415 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.55.0+ds-3 [225 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.55.0+ds-3 [54.6 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.55.0+ds-3 [35.4 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libpathplan4 amd64 2.42.4-2+b2 [42.8 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libgvc6 amd64 2.42.4-2+b2 [685 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libgvpr2 amd64 2.42.4-2+b2 [193 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 liblab-gamut1 amd64 2.42.4-2+b2 [198 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-3+b4 [59.0 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libxaw7 amd64 2:1.0.16-1 [212 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 graphviz amd64 2.42.4-2+b2 [618 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 libgpg-error0 amd64 1.51-3 [82.2 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 5.3.0-1+b1 [1676 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 195 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 xsltproc amd64 1.1.35-1.1+b1 [115 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 gtk-doc-tools all 1.34.0-2 [328 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-5+b1 [210 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libonig5 amd64 6.9.9-1+b1 [189 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libjq1 amd64 1.7.1-3+b1 [164 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 jq amd64 1.7.1-3+b1 [77.8 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-3 [59.5 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-3 [41.7 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-3 [42.0 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-3 [53.5 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-3 [126 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 libbackward-cpp-dev all 1.6-1 [34.3 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 uuid-dev amd64 2.40.2-14 [47.5 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 libblkid-dev amd64 2.40.2-14 [205 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-4 [10.6 MB] Get: 215 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83.0 amd64 1.83.0-4 [347 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83-dev amd64 1.83.0-4 [375 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Get: 218 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 liblzo2-2 amd64 2.10-3+b1 [55.1 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 libcairo-script-interpreter2 amd64 1.18.2-2 [58.8 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 libpng-dev amd64 1.6.44-3 [366 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 libfreetype-dev amd64 2.13.3+dfsg-1 [622 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 libfontconfig-dev amd64 2.15.0-1.1+b1 [414 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 libffi-dev amd64 3.4.6-1 [60.6 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 libsepol-dev amd64 3.7-1 [370 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.44-5 [260 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 libpcre2-32-0 amd64 10.44-5 [248 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 libpcre2-posix3 amd64 10.44-5 [60.4 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 libpcre2-dev amd64 10.44-5 [790 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 libselinux1-dev amd64 3.7-3+b1 [160 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 libmount-dev amd64 2.40.2-14 [29.3 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 libsysprof-capture-4-dev amd64 47.2-1 [47.7 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 libgio-2.0-dev amd64 2.82.4-1 [1678 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 libglib2.0-data all 2.82.4-1 [1276 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 libglib2.0-bin amd64 2.82.4-1 [127 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 libgio-2.0-dev-bin amd64 2.82.4-1 [163 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 libglib2.0-dev-bin amd64 2.82.4-1 [52.0 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 libglib2.0-dev amd64 2.82.4-1 [52.7 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 libpixman-1-dev amd64 0.44.0-3 [11.4 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 x11proto-dev all 2024.1-1 [603 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 x11proto-core-dev all 2024.1-1 [3312 B] Get: 248 http://deb.debian.org/debian unstable/main amd64 libice-dev amd64 2:1.1.1-1 [73.8 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 libsm-dev amd64 2:1.2.4-1 [37.7 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 libxau-dev amd64 1:1.0.11-1 [23.6 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 libxdmcp-dev amd64 1:1.1.5-1 [44.3 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 libxcb1-dev amd64 1.17.0-2+b1 [181 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 libx11-dev amd64 2:1.8.10-2 [891 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 libxcb-render0-dev amd64 1.17.0-2+b1 [118 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0-dev amd64 1.17.0-2+b1 [108 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 libxext-dev amd64 2:1.3.4-1+b3 [104 kB] Get: 258 http://deb.debian.org/debian unstable/main amd64 libxrender-dev amd64 1:0.9.10-1.1+b3 [35.9 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 libcairo2-dev amd64 1.18.2-2 [43.0 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.8-2 [449 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.8-2 [449 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.19.0-3+b3 [98.9 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10-1+b1 [1317 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.8-2 [1391 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-3 [15.7 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.5.19+dfsg-1 [303 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.6.0-2 [88.5 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.9.1-1 [23.1 kB] Get: 276 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.9.1-1 [167 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.4.0-2 [2790 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.11.1-1 [474 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.22-1 [55.8 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 libdisorder-dev amd64 0.0.2+git20130809.8062ee1-4+b2 [4912 B] Get: 285 http://deb.debian.org/debian unstable/main amd64 libdivsufsort3 amd64 2.0.1-6+b1 [45.9 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 libdivsufsort-dev amd64 2.0.1-6+b1 [19.1 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 libelf-dev amd64 0.192-4 [93.2 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 libdw-dev amd64 0.192-4 [335 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 libfastahack-dev amd64 1.0.0+dfsg-11+b2 [27.9 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 libfml0 amd64 0.1+git20221215.85f159e-1 [70.1 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 libfml-dev amd64 0.1+git20221215.85f159e-1 [82.0 kB] Get: 293 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-12 [836 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get: 296 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.20+ds-2 [1701 kB] Get: 297 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-5+b1 [10.4 MB] Get: 298 http://deb.debian.org/debian unstable/main amd64 libjansson-dev amd64 2.14-2+b3 [43.2 kB] Get: 299 http://deb.debian.org/debian unstable/main amd64 libjemalloc2 amd64 5.3.0-2+b2 [275 kB] Get: 300 http://deb.debian.org/debian unstable/main amd64 libjemalloc-dev amd64 5.3.0-2+b2 [491 kB] Get: 301 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get: 302 http://deb.debian.org/debian unstable/main amd64 libxxhash-dev amd64 0.8.3-2 [81.0 kB] Get: 303 http://deb.debian.org/debian unstable/main amd64 liblz4-dev amd64 1.9.4-4 [83.0 kB] Get: 304 http://deb.debian.org/debian unstable/main amd64 libmhash2 amd64 0.9.9.9-10 [92.4 kB] Get: 305 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get: 306 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5-2+b1 [351 kB] Get: 307 http://deb.debian.org/debian unstable/main amd64 libpaper2 amd64 2.2.5-0.3 [16.3 kB] Get: 308 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 2.2.5-0.3 [16.1 kB] Get: 309 http://deb.debian.org/debian unstable/main amd64 libprotobuf32t64 amd64 3.21.12-10+b2 [982 kB] Get: 310 http://deb.debian.org/debian unstable/main amd64 libprotobuf-lite32t64 amd64 3.21.12-10+b2 [274 kB] Get: 311 http://deb.debian.org/debian unstable/main amd64 libprotobuf-dev amd64 3.21.12-10+b2 [1331 kB] Get: 312 http://deb.debian.org/debian unstable/main amd64 libprotoc32t64 amd64 3.21.12-10+b2 [921 kB] Get: 313 http://deb.debian.org/debian unstable/main amd64 libprotoc-dev amd64 3.21.12-10+b2 [1024 kB] Get: 314 http://deb.debian.org/debian unstable/main amd64 libyajl2 amd64 2.1.0-5+b2 [23.3 kB] Get: 315 http://deb.debian.org/debian unstable/main amd64 libraptor2-0 amd64 2.0.16-4+b1 [177 kB] Get: 316 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [795 kB] Get: 317 http://deb.debian.org/debian unstable/main amd64 libxslt1-dev amd64 1.1.35-1.1+b1 [346 kB] Get: 318 http://deb.debian.org/debian unstable/main amd64 libyajl-dev amd64 2.1.0-5+b2 [32.0 kB] Get: 319 http://deb.debian.org/debian unstable/main amd64 libraptor2-dev amd64 2.0.16-4+b1 [211 kB] Get: 320 http://deb.debian.org/debian unstable/main amd64 librasqal3t64 amd64 0.9.33-2.1+b2 [191 kB] Get: 321 http://deb.debian.org/debian unstable/main amd64 librasqal3-dev amd64 0.9.33-2.1+b2 [227 kB] Get: 322 http://deb.debian.org/debian unstable/main amd64 librdf0t64 amd64 1.0.17-4+b1 [107 kB] Get: 323 http://deb.debian.org/debian unstable/main amd64 librdf0-dev amd64 1.0.17-4+b1 [238 kB] Get: 324 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.2-2 [467 kB] Get: 325 http://deb.debian.org/debian unstable/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12+b2 [36.8 kB] Get: 326 http://deb.debian.org/debian unstable/main amd64 libsmithwaterman-dev amd64 0.0+git20160702.2610e25-12+b2 [41.4 kB] Get: 327 http://deb.debian.org/debian unstable/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 328 http://deb.debian.org/debian unstable/main amd64 libssw0 amd64 1.1-15+b2 [21.8 kB] Get: 329 http://deb.debian.org/debian unstable/main amd64 libssw-dev amd64 1.1-15+b2 [24.6 kB] Get: 330 http://deb.debian.org/debian unstable/main amd64 libtabixpp0t64 amd64 1.1.2-2.1+b1 [10.3 kB] Get: 331 http://deb.debian.org/debian unstable/main amd64 libtabixpp-dev amd64 1.1.2-2.1+b1 [9528 B] Get: 332 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get: 333 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 334 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 335 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b3 [54.6 kB] Get: 336 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 337 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get: 338 http://deb.debian.org/debian unstable/main amd64 libtsl-hopscotch-map-dev all 2.3.1-1 [36.6 kB] Get: 339 http://deb.debian.org/debian unstable/main amd64 libwfa2-0 amd64 2.3.3-4+b1 [61.1 kB] Get: 340 http://deb.debian.org/debian unstable/main amd64 libvcflib2 amd64 1.0.9+dfsg1-3+b2 [194 kB] Get: 341 http://deb.debian.org/debian unstable/main amd64 libwfa2-dev amd64 2.3.3-4+b1 [79.7 kB] Get: 342 http://deb.debian.org/debian unstable/main amd64 libvcflib-dev amd64 1.0.9+dfsg1-3+b2 [77.8 kB] Get: 343 http://deb.debian.org/debian unstable/main amd64 zip amd64 3.0-14 [233 kB] Get: 344 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB] Get: 345 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 346 http://deb.debian.org/debian unstable/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Get: 347 http://deb.debian.org/debian unstable/main amd64 r-cran-littler amd64 0.3.20-2 [103 kB] Get: 348 http://deb.debian.org/debian unstable/main amd64 littler all 0.3.20-2 [16.0 kB] Get: 349 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get: 350 http://deb.debian.org/debian unstable/main amd64 r-cran-rcpp amd64 1.0.13-1-1 [2074 kB] Get: 351 http://deb.debian.org/debian unstable/main amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] Get: 352 http://deb.debian.org/debian unstable/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB] Get: 353 http://deb.debian.org/debian unstable/main amd64 r-cran-glue amd64 1.8.0-1 [165 kB] Get: 354 http://deb.debian.org/debian unstable/main amd64 r-cran-rlang amd64 1.1.4-1 [1712 kB] Get: 355 http://deb.debian.org/debian unstable/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get: 356 http://deb.debian.org/debian unstable/main amd64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Get: 357 http://deb.debian.org/debian unstable/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get: 358 http://deb.debian.org/debian unstable/main amd64 r-cran-mass amd64 7.3-64-1 [1113 kB] Get: 359 http://deb.debian.org/debian unstable/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get: 360 http://deb.debian.org/debian unstable/main amd64 r-cran-nlme amd64 3.1.166-1 [2330 kB] Get: 361 http://deb.debian.org/debian unstable/main amd64 r-cran-matrix amd64 1.7-1-1 [4138 kB] Get: 362 http://deb.debian.org/debian unstable/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get: 363 http://deb.debian.org/debian unstable/main amd64 r-cran-farver amd64 2.1.2-1 [1411 kB] Get: 364 http://deb.debian.org/debian unstable/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get: 365 http://deb.debian.org/debian unstable/main amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1716 kB] Get: 366 http://deb.debian.org/debian unstable/main amd64 r-cran-munsell all 0.5.1-1 [237 kB] Get: 367 http://deb.debian.org/debian unstable/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get: 368 http://deb.debian.org/debian unstable/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get: 369 http://deb.debian.org/debian unstable/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get: 370 http://deb.debian.org/debian unstable/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get: 371 http://deb.debian.org/debian unstable/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get: 372 http://deb.debian.org/debian unstable/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get: 373 http://deb.debian.org/debian unstable/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get: 374 http://deb.debian.org/debian unstable/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get: 375 http://deb.debian.org/debian unstable/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get: 376 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 377 http://deb.debian.org/debian unstable/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get: 378 http://deb.debian.org/debian unstable/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get: 379 http://deb.debian.org/debian unstable/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get: 380 http://deb.debian.org/debian unstable/main amd64 r-cran-gridbase all 0.4-7-5 [163 kB] Get: 381 http://deb.debian.org/debian unstable/main amd64 libvcflib-tools amd64 1.0.9+dfsg1-3+b2 [660 kB] Get: 382 http://deb.debian.org/debian unstable/main amd64 protobuf-compiler amd64 3.21.12-10+b2 [84.8 kB] Get: 383 http://deb.debian.org/debian unstable/main amd64 pv amd64 1.9.25-1 [105 kB] Get: 384 http://deb.debian.org/debian unstable/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Get: 385 http://deb.debian.org/debian unstable/main amd64 raptor2-utils amd64 2.0.16-4+b1 [35.0 kB] Get: 386 http://deb.debian.org/debian unstable/main amd64 rasqal-utils amd64 0.9.33-2.1+b2 [43.8 kB] Get: 387 http://deb.debian.org/debian unstable/main amd64 rs amd64 20200313-1 [15.5 kB] Get: 388 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.20-3 [653 kB] Get: 389 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.20+ds-2 [486 kB] Get: 390 http://deb.debian.org/debian unstable/main amd64 xxd amd64 2:9.1.0967-1+b1 [98.7 kB] Fetched 269 MB in 8s (33.4 MB/s) Preconfiguring packages ... 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 ... 19848 files and directories currently installed.) Preparing to unpack .../archives/m4_1.4.19-5_amd64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package flex. Preparing to unpack .../flex_2.6.4-8.2+b4_amd64.deb ... Unpacking flex (2.6.4-8.2+b4) ... Selecting previously unselected package readline-common. Preparing to unpack .../readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../libreadline8t64_8.2-6_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 (8.2-6) ... 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 (8.2-6) ... Setting up libreadline8t64:amd64 (8.2-6) ... 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 ... 20073 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 libproc2-0:amd64. Preparing to unpack .../1-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 .../2-procps_2%3a4.0.4-6_amd64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../3-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package ucf. Preparing to unpack .../4-ucf_3.0046_all.deb ... Moving old data out of the way Unpacking ucf (3.0046) ... Selecting previously unselected package libdebuginfod-common. Preparing to unpack .../5-libdebuginfod-common_0.192-4_all.deb ... Unpacking libdebuginfod-common (0.192-4) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../6-liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../7-libpython3.13-minimal_3.13.1-3_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.1-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../8-libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../9-python3.13-minimal_3.13.1-3_amd64.deb ... Unpacking python3.13-minimal (3.13.1-3) ... Setting up libpython3.13-minimal:amd64 (3.13.1-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.1-3) ... 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 ... 20858 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.1-1_amd64.deb ... Unpacking python3-minimal (3.13.1-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... 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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 libxft2:amd64. Preparing to unpack .../311-libxft2_2.3.6-1+b3_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b3) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../312-libxss1_1%3a1.2.3-1+b3_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1+b3) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../313-libtk8.6_8.6.15-1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.15-1) ... Selecting previously unselected package libtsl-hopscotch-map-dev. Preparing to unpack .../314-libtsl-hopscotch-map-dev_2.3.1-1_all.deb ... Unpacking libtsl-hopscotch-map-dev (2.3.1-1) ... 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Use glob.glob and pass a directory to its root_dir argument instead. for fn in glob1(directory, "%s.*" % fname): /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. for fn in glob1(directory, "%s.*" % fname): Setting up libidn2-0:amd64 (2.3.7-2+b1) ... Setting up libpaper-utils (2.2.5-0.3) ... Setting up opensp (1.5.2-15.1) ... Setting up libngtcp2-dev:amd64 (1.9.1-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up libffi-dev:amd64 (3.4.6-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libprotobuf-dev:amd64 (3.21.12-10+b2) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libxdmcp-dev:amd64 (1:1.1.5-1) ... Setting up libxml2-dev:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libglib2.0-0t64:amd64 (2.82.4-1) ... No schema files found: doing nothing. Setting up python3-packaging (24.2-1) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up x11proto-core-dev (2024.1-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libelf-dev:amd64 (0.192-4) ... Setting up liblz4-dev:amd64 (1.9.4-4) ... Setting up libsmithwaterman-dev:amd64 (0.0+git20160702.2610e25-12+b2) ... Setting up libgav1-1:amd64 (0.19.0-3) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up ucf (3.0046) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libidn2-dev:amd64 (2.3.7-2+b1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libgvpr2:amd64 (2.42.4-2+b2) ... Setting up libprotoc-dev:amd64 (3.21.12-10+b2) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up jq (1.7.1-3+b1) ... Setting up libxslt1.1:amd64 (1.1.35-1.1+b1) ... Setting up libharfbuzz0b:amd64 (10.1.0-2) ... Setting up libgts-0.7-5t64:amd64 (0.7.6+darcs121130-5.2+b1) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up libsm6:amd64 (2:1.2.4-1) ... Setting up libarchive13t64:amd64 (3.7.4-1.1) ... Setting up libmount-dev:amd64 (2.40.2-14) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libclang-cpp19 (1:19.1.6-1+b1) ... Setting up libgnutls30t64:amd64 (3.8.8-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up libgnutls-openssl27t64:amd64 (3.8.8-2) ... 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 libgio-2.0-dev-bin (2.82.4-1) ... Setting up libxft2:amd64 (2.3.6-1+b3) ... Setting up libgio-2.0-dev:amd64 (2.82.4-1) ... Setting up libxcb1-dev:amd64 (1.17.0-2+b1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up libxslt1-dev:amd64 (1.1.35-1.1+b1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up libdebuginfod-common (0.192-4) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up libgirepository-2.0-0:amd64 (2.82.4-1) ... 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 (1.55.0+ds-3) ... Setting up python3-typeguard (4.4.1-1) ... Setting up xsltproc (1.1.35-1.1+b1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libx11-dev:amd64 (2:1.8.10-2) ... Setting up libglib2.0-bin (2.82.4-1) ... 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 libldap-2.5-0:amd64 (2.5.19+dfsg-1) ... Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libfreetype-dev:amd64 (2.13.3+dfsg-1) ... Setting up libxcb-shm0-dev:amd64 (1.17.0-2+b1) ... Setting up python3-inflect (7.3.1-2) ... Setting up doxygen (1.9.8+ds-2+b3) ... Setting up libgnutls-dane0t64:amd64 (3.8.8-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:amd64 (1.21.3-3) ... Setting up libldap-dev:amd64 (2.5.19+dfsg-1) ... Setting up libraqm0:amd64 (0.10.2-1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b2) ... Setting up libxcb-render0-dev:amd64 (1.17.0-2+b1) ... Setting up libxext-dev:amd64 (2:1.3.4-1+b3) ... Setting up python3-lxml:amd64 (5.3.0-1+b1) ... Setting up libcairo-gobject2:amd64 (1.18.2-2) ... Setting up libpangoft2-1.0-0:amd64 (1.55.0+ds-3) ... Setting up libxrender-dev:amd64 (1:0.9.10-1.1+b3) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up libpangocairo-1.0-0:amd64 (1.55.0+ds-3) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-3) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up libgnutls28-dev:amd64 (3.8.8-2) ... Setting up libcairo-script-interpreter2:amd64 (1.18.2-2) ... Setting up libxmu6:amd64 (2:1.1.3-3+b4) ... Setting up girepository-tools:amd64 (2.82.4-1) ... Setting up libcurl4t64:amd64 (8.11.1-1) ... Setting up libkdb5-10t64:amd64 (1.21.3-3) ... Setting up libfontconfig-dev:amd64 (2.15.0-1.1+b1) ... Setting up libcurl3t64-gnutls:amd64 (8.11.1-1) ... Setting up debhelper (13.23) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.9.1-1) ... Setting up libxaw7:amd64 (2:1.0.16-1) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up r-base-core (4.4.2-1) ... Creating config file /etc/R/Renviron with new version Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... 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 cmake (3.31.3-1) ... Setting up libhts3t64:amd64 (1.20+ds-2) ... 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 krb5-multidev:amd64 (1.21.3-3) ... Setting up r-cran-littler (0.3.20-2) ... Setting up libglib2.0-dev-bin (2.82.4-1) ... Setting up r-cran-rcpp (1.0.13-1-1) ... Setting up libdebuginfod1t64:amd64 (0.192-4) ... Setting up r-cran-rlang (1.1.4-1) ... Setting up r-cran-gridbase (0.4-7-5) ... Setting up littler (0.3.20-2) ... Setting up r-cran-withr (3.0.2+dfsg-1) ... Setting up libraptor2-0:amd64 (2.0.16-4+b1) ... Setting up raptor2-utils (2.0.16-4+b1) ... Setting up r-cran-fansi (1.0.5-1) ... Setting up r-cran-mass (7.3-64-1) ... Setting up librasqal3t64:amd64 (0.9.33-2.1+b2) ... Setting up librdf0t64:amd64 (1.0.17-4+b1) ... Setting up r-cran-glue (1.8.0-1) ... Setting up r-cran-cli (3.6.3-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up samtools (1.20-3) ... 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 r-cran-colorspace (2.1-1+dfsg-1) ... Setting up libglib2.0-dev:amd64 (2.82.4-1) ... 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 r-cran-matrix (1.7-1-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up libtabixpp0t64:amd64 (1.1.2-2.1+b1) ... Setting up libcairo2-dev:amd64 (1.18.2-2) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up rasqal-utils (0.9.33-2.1+b2) ... Setting up elfutils (0.192-4) ... 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 (8.11.1-1) ... Setting up libvcflib2:amd64 (1.0.9+dfsg1-3+b2) ... Setting up r-cran-scales (1.3.0-1) ... Setting up libraptor2-dev:amd64 (2.0.16-4+b1) ... 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 librdf0-dev (1.0.17-4+b1) ... Setting up libtabixpp-dev:amd64 (1.1.2-2.1+b1) ... Setting up libvcflib-dev:amd64 (1.0.9+dfsg1-3+b2) ... Setting up libheif-plugin-dav1d:amd64 (1.19.5-1) ... Setting up libheif-plugin-libde265:amd64 (1.19.5-1) ... Setting up libheif1:amd64 (1.19.5-1) ... Setting up libgd3:amd64 (2.3.3-12+b1) ... Setting up libgvc6 (2.42.4-2+b2) ... Setting up graphviz (2.42.4-2+b2) ... Processing triggers for libc-bin (2.40-5) ... 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 (1.34.0-2) ... Processing triggers for ca-certificates (20241223) ... 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 -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 rm -rf ../bin ../lib make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' 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' rm -rf ./obj/*.o rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -m${SIMD}" && export CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -m${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 -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 -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 -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 -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* 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. cp deps/BBHash/BooPHF.h /build/reproducible-path/vg-1.59.0+ds/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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc cp -r deps/sparsepp/sparsepp include/ make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' rm -Rf include/dynamic.hpp include/dynamic . ./source_me.sh && cp -r deps/mio/include/mio /build/reproducible-path/vg-1.59.0+ds/include/ 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' rm -Rf include/google/protobuf deps/protobuf 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 -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 . ./source_me.sh && cp -r deps/atomic_queue/include/atomic_queue/* /build/reproducible-path/vg-1.59.0+ds/include/ 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/structures' if [ ! -d bin ]; then mkdir -p bin; fi touch lib/cleaned_old_protobuf_v003 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/* 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" && cmake -DCMAKE_VERBOSE_MAKEFILE=ON .. && make cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ . ./source_me.sh && cp -r deps/ips4o/ips4o* /build/reproducible-path/vg-1.59.0+ds/include/ make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make all touch: cannot touch 'lib/cleaned_old_protobuf_v003': No such file or directory cd quicktree_1.1 && make all CC="gcc -std=c99" make[2]: *** [Makefile:574: lib/cleaned_old_protobuf_v003] Error 1 make[2]: *** Waiting for unfinished jobs.... WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' if [ ! -d obj ]; then mkdir -p obj; fi 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/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 -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 -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 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 -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 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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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 -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 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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -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 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 -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 -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 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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -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 find bin obj lib -type f -delete 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 -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 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -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 -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 -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 make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi 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 -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 -- Setting build type to 'Release' as none was specified. if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi 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 tif [ ! -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 he 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 -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 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 -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 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -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 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./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 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 | } | ^ -- The CXX 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 -- Detecting C compiler ABI info -- Detecting C compiler ABI info -- 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 -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - 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 | } | ^ -- 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 -- Detecting CXX compiler ABI info - done -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info - done -- Configuring done (0.9s) -- Generating done (0.0s) -- 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/g++ - skipped -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting CXX compile features -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compile features - done make[3]: Entering directory '/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 libhandlegraph is root project or external_project -- Configuring done (0.9s) src/gssw.c: In function ‘gssw_graph_print’: -- Detecting CXX compiler ABI info - done 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 -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build 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[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 src/gssw.c: In function ‘gssw_print_graph_cigar’: /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 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 [ 16%] Building CXX object CMakeFiles/kff.dir/kff_io.cpp.o -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done make -f CMakeFiles/Makefile2 all src/gssw.c: In function ‘gssw_create_seed_byte’: 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=" 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 Building in Release mode make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -- Configuring done (1.0s) 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/deletable_handle_graph.cpp.o [ 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 -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 /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 -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 [ 14%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o [ 14%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o [ 20%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o [ 20%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o [ 25%] 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 -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 [ 28%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o [ 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp [ 34%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o [ 37%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_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 -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 [ 40%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_metadata.cpp -- Generating done (0.0s) [ 42%] Building CXX 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp -- Build files have been written to: /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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o [ 48%] 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_handle_graph.cpp [ 51%] 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/ranked_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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/serializable.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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 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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 -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 /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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-ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/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 [ 60%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/apply_orientations.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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp [ 62%] 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 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-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 -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 [ 74%] Building CXX object 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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 [ 6%] Building CXX object CMakeFiles/debug.dir/debug.cpp.o /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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/debug.dir/debug.cpp.o -MF CMakeFiles/debug.dir/debug.cpp.o.d -o CMakeFiles/debug.dir/debug.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/debug.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' 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 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 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 cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp 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CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.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 -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 cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h make[5]: Leaving directory '/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' make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/depend 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/rle_lz77_v2.dir/DependInfo.cmake "--color=" 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 [ 12%] Building CXX object CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o /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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -MF CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o.d -o CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/rle_lz77_v1.cpp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o cp inc/sonLibHash.h ../lib/sonLibHash.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 -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 mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/build cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' 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 [ 18%] Building CXX object CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h /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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -MF CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o.d -o CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/rle_lz77_v2.cpp cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success 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 mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp 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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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 make -f CMakeFiles/h0_lz77.dir/build.make CMakeFiles/h0_lz77.dir/depend 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/h0_lz77.dir/DependInfo.cmake "--color=" make[5]: Leaving 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' [ 25%] Building CXX object CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o /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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -MF CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o.d -o CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/h0_lz77.cpp make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/depend 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/rle_bwt.dir/DependInfo.cmake "--color=" [ 82%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o make -f CMakeFiles/cw-bwt.dir/build.make CMakeFiles/cw-bwt.dir/depend /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 -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 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/cw-bwt.dir/DependInfo.cmake "--color=" make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.dir/depend [ 85%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o 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 -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 cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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/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=" /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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -MF CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o.d -o CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/cw-bwt.cpp [ 43%] Building CXX object 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'/build/reproducible-path/vg-1.59.0+ds/deps/structures' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:622: lib/libstructures.a] Error 1 [ 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 -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 [ 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 -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 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)) { | ^ 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 -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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. -lm -lz -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- 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 -- Looking for C++ include cstdio - found -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -- Configuring done (3.9s) make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' ar: /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a: No such file or directory make[2]: *** [Makefile:515: lib/libssw.a] Error 1 -- Generating done (0.3s) 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))); | ^ -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build src/gssw.c: In function ‘gssw_sw_software_word’: src/gssw.c:1117:5: warning: ‘__builtin_memcpy’ writing between 18446744069414584336 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 1117 | memcpy(scratch, to_unswizzle, size * sizeof(int16_t)); | ^ In function ‘unswizzle_word’, inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/bits.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o [ 12%] 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 -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 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 -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 [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.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 -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 [ 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 -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_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 -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 [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o [ 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 -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 [ 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 -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 -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 [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/io.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 -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 [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.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 -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 [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o [ 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 -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 [ 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 -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 -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 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 -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 [ 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 -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 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 -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 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 -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 [ 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 -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 -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 [ 87%] 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 -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 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 -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 [ 87%] 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 -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 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 -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 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 -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 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 -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 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 -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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 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 [ 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 -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 -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 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/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 -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 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 [ 56%] Linking CXX executable debug /usr/bin/cmake -E cmake_link_script CMakeFiles/debug.dir/link.txt --verbose=1 [ 33%] Built target kff [ 50%] Building CXX object CMakeFiles/kff_example.dir/main.cpp.o [ 66%] Building CXX object benchmarks/CMakeFiles/reader_bench.dir/reader.cpp.o /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 -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 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]: 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 [ 56%] Built target debug 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 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 &= | ^~~~~ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:637: lib/libsublinearLS.a] Error 1 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 83%] Linking CXX executable reader_bench cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 83%] Built target reader_bench 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 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 -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 -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 -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 [100%] Linking CXX executable kff_example [100%] Built target kff_example 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' cp: cannot stat '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:598: lib/libgssw.a] Error 1 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 -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' [ 62%] Built target wm_string cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 68%] Linking CXX executable benchmark /usr/bin/cmake -E cmake_link_script CMakeFiles/benchmark.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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' [ 81%] Linking CXX executable rle_lz77_v2 [ 81%] Linking CXX executable cw-bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/cw-bwt.dir/link.txt --verbose=1 /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v2.dir/link.txt --verbose=1 [ 81%] Built target benchmark 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 -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 /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 -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' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 81%] Built target rle_lz77_v2 [ 81%] Built target cw-bwt 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' [ 87%] 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 [ 93%] Linking CXX executable rle_lz77_v1 /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 -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 /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/DYNAMIC/build' [ 93%] Built target rle_bwt 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 -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' [ 93%] Built target rle_lz77_v1 [ 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' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Linking CXX static library libhandlegraph.a [100%] Linking CXX shared library libhandlegraph.so /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 [100%] Linking CXX executable h0_lz77 /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/cmake -E cmake_link_script CMakeFiles/h0_lz77.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 -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 /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 -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/DYNAMIC/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 h0_lz77 [100%] Built target handlegraph_shared 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[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/ 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 /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 /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' 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 -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' [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: "" CMake Error at cmake_install.cmake:52 (file): file INSTALL destination: /build/reproducible-path/vg-1.59.0+ds/lib is not a directory. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[2]: *** [Makefile:594: lib/libhandlegraph.a] Error 2 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); | ^~~~~~~~~~~~ [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 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 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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 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 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/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" CMake Error at cmake_install.cmake:46 (file): file cannot create directory: /build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig. Maybe need administrative privileges. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' ERROR: Installation failed. make[2]: *** [Makefile:511: lib/libsdsl.a] Error 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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest 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' cp: cannot stat '/build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a': Not a directory make[2]: *** [Makefile:616: lib/libsonlib.a] Error 1 make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_build: error: make -j42 "INSTALL=install --strip-program=true" SFX=-avx2 all test/build_graph bin/shuf returned exit code 2 make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+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 -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 CMake Error at CMakeModules/cmake_uninstall.cmake:2 (MESSAGE): Cannot find install manifest: "/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/install_manifest.txt" make[6]: *** [CMakeFiles/uninstall-sdsl.dir/build.make:73: CMakeFiles/uninstall-sdsl] Error 1 make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[5]: *** [CMakeFiles/Makefile2:397: CMakeFiles/uninstall-sdsl.dir/all] Error 2 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[4]: *** [CMakeFiles/Makefile2:404: CMakeFiles/uninstall-sdsl.dir/rule] Error 2 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: *** [Makefile:172: uninstall-sdsl] Error 2 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' 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 -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 -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 -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* 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 -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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc . ./source_me.sh && cp deps/mmmultimap/src/mmmultimap.hpp deps/mmmultimap/src/mmmultiset.hpp /build/reproducible-path/vg-1.59.0+ds/include/ cd ./deps/lru_cache && cp *.h* /build/reproducible-path/vg-1.59.0+ds/include/ make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' cp deps/sha1/*.h* /build/reproducible-path/vg-1.59.0+ds/include/ Library will be installed in '/build/reproducible-path/vg-1.59.0+ds' rm -Rf include/google/protobuf deps/protobuf cp deps/progress_bar/progress_bar.hpp /build/reproducible-path/vg-1.59.0+ds/include make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd externalTools && make all 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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+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 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/* if [ ! -d obj ]; then mkdir -p obj; fi make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make all WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. cd quicktree_1.1 && make all CC="gcc -std=c99" touch lib/cleaned_old_protobuf_v003 if [ ! -d lib ]; then mkdir -p lib; fi touch: cannot touch 'lib/cleaned_old_protobuf_v003': No such file or directory 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[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 -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 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 -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' 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 -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 make[2]: *** [Makefile:574: lib/cleaned_old_protobuf_v003] Error 1 make[2]: *** Waiting for unfinished jobs.... 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 -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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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 -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 -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 -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 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[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -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 if [ ! -d obj ]; then mkdir -p obj; fi 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 -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 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/union_find.cpp -o obj/union_find.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 -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 -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 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/stable_double.cpp -o obj/stable_double.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 -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 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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 /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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 ./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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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 C 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 | } | ^ 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/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’: 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 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 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 CXX compiler identification is GNU 14.2.0 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 -- Detecting C compiler ABI info - done -- Detecting C compiler ABI info - 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 -- Check for working C compiler: /usr/bin/gcc - skipped make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' -- Detecting C compile features -- Detecting C compile features - done 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 mv ../lib/avl.h.tmp ../lib/avl.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h mv ../lib/commonC.h.tmp ../lib/commonC.h mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/jsmn.h ../lib/jsmn.h.tmp cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h 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 cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.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/sonLibRandom.h.tmp ../lib/sonLibRandom.h mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stJson.h ../lib/stJson.h.tmp cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h 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 cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp 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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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 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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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 -- The C compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:622: lib/libstructures.a] Error 1 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 -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++ 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 CXX compiler ABI info - done -- Detecting CXX compiler ABI info - done -- Detecting CXX compiler ABI info - done 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 -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting CXX compile features - done libhandlegraph is root project or external_project -- Detecting C compiler ABI info -- Configuring done (2.7s) -- Configuring done (2.7s) -- Generating done (0.0s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build -- 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/kff-cpp-api/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' [ 16%] Building CXX object CMakeFiles/kff.dir/kff_io.cpp.o [ 2%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o [ 5%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o [ 8%] 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 -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 [ 11%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o [ 20%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o [ 17%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o [ 20%] 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 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CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_metadata.cpp [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o [ 28%] 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 -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/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 [ 31%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.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 -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/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 [ 37%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o [ 34%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.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 -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/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 /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 -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/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 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-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 [ 88%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/chop.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 -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/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 [ 91%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o [ 94%] 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 -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 /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 -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 /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 -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 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' ar: /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a: No such file or directory make[2]: *** [Makefile:515: lib/libssw.a] Error 1 -- 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 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- 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 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 -- Looking for C++ include cstdio - found -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -- Configuring done (3.8s) -- 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 -f CMakeFiles/Makefile2 sdsl cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 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 [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o [ 25%] 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 -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 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 -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 [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o [ 37%] 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 -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 -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 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 -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 -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 [ 37%] 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 -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 -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 [ 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 -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 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 -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 [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.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 [ 62%] 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 -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 [ 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 -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 [ 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 -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 -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 -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 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 -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 [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.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 -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 [ 75%] 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 -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 [ 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 -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 -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 -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 [ 75%] 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 -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 -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 [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o [ 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 -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 [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.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 -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 -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 -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 -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 -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 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 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 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/sublinear-Li-Stephens' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:637: lib/libsublinearLS.a] Error 1 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 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 -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 -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 -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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 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 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 &= | ^~~~~ [ 33%] Linking CXX static library libkff.a cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 33%] Built target kff cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 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 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:598: lib/libgssw.a] Error 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 [ 83%] Linking CXX executable reader_bench cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Built target kff_example 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 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 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 -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' [ 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 -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' [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[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' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 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: "" CMake Error at cmake_install.cmake:52 (file): file INSTALL destination: /build/reproducible-path/vg-1.59.0+ds/lib is not a directory. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[2]: *** [Makefile:594: lib/libhandlegraph.a] Error 2 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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 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' 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: "Release" CMake Error at cmake_install.cmake:46 (file): file cannot create directory: /build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig. Maybe need administrative privileges. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' ERROR: Installation failed. make[2]: *** [Makefile:511: lib/libsdsl.a] Error 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 -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 -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 -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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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 mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest 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' cp: cannot stat '/build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a': Not a directory make[2]: *** [Makefile:616: lib/libsonlib.a] Error 1 make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_build: error: make -j42 "INSTALL=install --strip-program=true" SFX=-avx all test/build_graph bin/shuf returned exit code 2 make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+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 -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 CMake Error at CMakeModules/cmake_uninstall.cmake:2 (MESSAGE): Cannot find install manifest: "/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/install_manifest.txt" make[6]: *** [CMakeFiles/uninstall-sdsl.dir/build.make:73: CMakeFiles/uninstall-sdsl] Error 1 make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[5]: *** [CMakeFiles/Makefile2:397: CMakeFiles/uninstall-sdsl.dir/all] Error 2 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[4]: *** [CMakeFiles/Makefile2:404: CMakeFiles/uninstall-sdsl.dir/rule] Error 2 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: *** [Makefile:172: uninstall-sdsl] Error 2 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' 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 -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 -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 -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 -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 -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 -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 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 -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/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 -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 rm -Rf include/google/protobuf deps/protobuf 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' touch: cannot touch 'lib/cleaned_old_protobuf_v003': No such file or directory make[2]: *** [Makefile:574: lib/cleaned_old_protobuf_v003] Error 1 make[2]: *** Waiting for unfinished jobs.... 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 -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 make[3]: Leaving 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 -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[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 -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 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c gcc -std=c99 -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 -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 -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 make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; 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 -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 /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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -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 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 -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 if [ ! -d lib ]; then mkdir -p lib; fi 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 -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 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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/stable_double.cpp -o obj/stable_double.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 -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 -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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -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 -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 -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 -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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -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 -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/tree.c: In function ‘read_newhampshire_Tnode’: ./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/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./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: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 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. /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 src/gssw.c: In function ‘gssw_print_graph_cigar’: -- The CXX compiler identification is GNU 14.2.0 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 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info src/gssw.c: In function ‘gssw_create_seed_byte’: -- Detecting C compiler ABI info 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 -- The C compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Check for working C compiler: /usr/bin/gcc - 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 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 CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done (0.6s) libhandlegraph is root project or external_project -- Configuring done (0.6s) -- 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' -- 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=" [ 16%] Building CXX object CMakeFiles/kff.dir/kff_io.cpp.o 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' [ 11%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_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/dfs.cpp.o [ 11%] 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 -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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/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 -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/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 /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 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-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 [ 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 -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/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 [ 31%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_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 -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/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 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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 -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/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 [ 60%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o [ 62%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o [ 65%] 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 -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/apply_orientations.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/apply_orientations.cpp [ 68%] 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 -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_single_stranded.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_single_stranded.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 -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/count_walks.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/count_walks.cpp -- Detecting C compiler ABI info - done /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 -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/eades_algorithm.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/eades_algorithm.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 -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/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 [ 71%] Building CXX object 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 -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/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 -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done [ 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 -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 -- Compiler is recent enough to support C++14. -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG 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' [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' /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 -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 cd C && make all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.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 -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 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 cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h [ 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 -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 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 cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS 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 mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h [ 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 -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 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 mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h [ 88%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.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 -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 [ 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 -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 [ 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 -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 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 -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 -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 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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:622: lib/libstructures.a] Error 1 -- Performing Test HAVE_CXA_DEMANGLE 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 -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++ -- 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 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)) { | ^ -- Looking for C++ include cstdio - found 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' ar: /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a: No such file or directory make[2]: *** [Makefile:515: lib/libssw.a] Error 1 -- Configuring done (2.5s) cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- 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 -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_config.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.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 -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 -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 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 -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 [ 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 -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 [ 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 -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 [ 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 -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 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 -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 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 -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 -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 [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o [ 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 -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 [ 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 -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/io.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o [ 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 -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 [ 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 -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 [ 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 -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/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 -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 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 -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 [ 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 -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 -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 [ 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 -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/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 -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 [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.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 -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 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 -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 -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 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 -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 -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 -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 -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 [ 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 -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 [ 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 -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 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 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 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 33%] Built target kff [ 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 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 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 &= | ^~~~~ [ 83%] Linking CXX executable 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 [ 83%] Built target reader_bench 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' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:637: lib/libsublinearLS.a] Error 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 [100%] Linking CXX executable kff_example # 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 -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 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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%] Built target kff_example 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 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' cp: cannot stat '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:598: lib/libgssw.a] Error 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 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 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]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 97%] Linking CXX static library libhandlegraph.a [100%] Linking CXX shared library libhandlegraph.so /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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /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 -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 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%] 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[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 [ 97%] Built target handlegraph_static 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: "" CMake Error at cmake_install.cmake:52 (file): file INSTALL destination: /build/reproducible-path/vg-1.59.0+ds/lib is not a directory. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[2]: *** [Makefile:594: lib/libhandlegraph.a] Error 2 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 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 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 -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/ /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' 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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm [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=" mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+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" CMake Error at cmake_install.cmake:46 (file): file cannot create directory: /build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig. Maybe need administrative privileges. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' ERROR: Installation failed. make[2]: *** [Makefile:511: lib/libsdsl.a] Error 1 mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest 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' cp: cannot stat '/build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a': Not a directory make[2]: *** [Makefile:616: lib/libsonlib.a] Error 1 make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_build: error: make -j42 "INSTALL=install --strip-program=true" SFX=-sse4.1 all test/build_graph bin/shuf returned exit code 2 make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+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 -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 CMake Error at CMakeModules/cmake_uninstall.cmake:2 (MESSAGE): Cannot find install manifest: "/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/install_manifest.txt" make[6]: *** [CMakeFiles/uninstall-sdsl.dir/build.make:73: CMakeFiles/uninstall-sdsl] Error 1 make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[5]: *** [CMakeFiles/Makefile2:397: CMakeFiles/uninstall-sdsl.dir/all] Error 2 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[4]: *** [CMakeFiles/Makefile2:404: CMakeFiles/uninstall-sdsl.dir/rule] Error 2 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: *** [Makefile:172: uninstall-sdsl] Error 2 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' 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 -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 -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 -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 -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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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 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' 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 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. 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/* 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 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' touch: cannot touch 'lib/cleaned_old_protobuf_v003': No such file or directory make[2]: *** [Makefile:574: lib/cleaned_old_protobuf_v003] Error 1 make[2]: *** Waiting for unfinished jobs.... 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 -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]: 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' 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 -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 -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 -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 -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 -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 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 -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 /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 -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 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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -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 lib ]; then mkdir -p lib; fi 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 -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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.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 -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 -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 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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -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 -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 -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 -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 -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 -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 -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 -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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 C compiler identification is GNU 14.2.0 -- The C compiler identification is GNU 14.2.0 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 /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 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 -- The CXX 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 C compiler ABI info -- Detecting CXX compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compiler ABI info - done ar rc cuTest.a *.o ranlib cuTest.a -- Detecting CXX compiler ABI info - done rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' -- Detecting C compile features - done -- 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 -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- 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 CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting CXX compile features - done -- Detecting C compiler ABI info - done libhandlegraph is root project or external_project -- Configuring done (0.8s) -- Configuring done (0.8s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build -- 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 make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -- Check for working C compiler: /usr/bin/gcc - skipped /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 -- Detecting C compile features -- Detecting C compile features - 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 -- Compiler is recent enough to support C++14. -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG 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' [ 11%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_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/handle_graph.cpp.o [ 14%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o [ 11%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o [ 17%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_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 -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/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 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' [ 20%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.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 -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/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 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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 -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/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 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 [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o cp inc/hashTableC.h ../lib/hashTableC.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 -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/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 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 cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp 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 -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o cp inc/stSafeC.h ../lib/stSafeC.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 -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/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 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 cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -pipe -O3 -I. -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 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 -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/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 [ 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 -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/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 [ 88%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/chop.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 -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/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 [ 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 -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/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 [ 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 -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/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 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 -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++ -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success -- Performing Test HAVE_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)) { | ^ 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' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:622: lib/libstructures.a] Error 1 src/gssw.c: In function ‘gssw_sw_software_byte’: src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 277 | memcpy(scratch, to_unswizzle, size); | ^ In function ‘unswizzle_byte’, inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' ar: /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a: No such file or directory make[2]: *** [Makefile:515: lib/libssw.a] Error 1 -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- 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 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Looking for C++ include cstdio - found -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -- Configuring done (3.8s) 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))); | ^ -- 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' [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o [ 37%] 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 -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 [ 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 -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 -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 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 -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 -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 -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 -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 [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/io.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 -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 [ 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 -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 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 -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 [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o [ 62%] 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 -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 -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 [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o [ 75%] 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 -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 [ 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 -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 -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 [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.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 -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 [ 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 -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 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 -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 -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 [ 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 -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 [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o [ 87%] 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 -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 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 -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 [ 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 -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 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 -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 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 -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 -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 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 -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 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 -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 -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 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 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 [ 33%] Linking CXX static library libkff.a 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 [ 33%] Built target kff 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/sublinear-Li-Stephens' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:637: lib/libsublinearLS.a] Error 1 [ 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); | ^~~~~~~~~~ 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 -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 -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 -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 [ 83%] Built target 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[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:598: lib/libgssw.a] Error 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 [100%] Linking CXX executable kff_example cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Built target kff_example 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' [ 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' [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 /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 -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_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 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' 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); | ^~~~~~~~~~~~ [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=" 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' 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' [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 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: "" CMake Error at cmake_install.cmake:52 (file): file INSTALL destination: /build/reproducible-path/vg-1.59.0+ds/lib is not a directory. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[2]: *** [Makefile:594: lib/libhandlegraph.a] Error 2 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 [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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /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*' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 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 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/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" CMake Error at cmake_install.cmake:46 (file): file cannot create directory: /build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig. Maybe need administrative privileges. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' ERROR: Installation failed. make[2]: *** [Makefile:511: lib/libsdsl.a] Error 1 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 -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 -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 -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 -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 -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 mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest 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' cp: cannot stat '/build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a': Not a directory make[2]: *** [Makefile:616: lib/libsonlib.a] Error 1 make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_build: error: make -j42 "INSTALL=install --strip-program=true" SFX=-ssse3 all test/build_graph bin/shuf returned exit code 2 make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+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 -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 CMake Error at CMakeModules/cmake_uninstall.cmake:2 (MESSAGE): Cannot find install manifest: "/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/install_manifest.txt" make[6]: *** [CMakeFiles/uninstall-sdsl.dir/build.make:73: CMakeFiles/uninstall-sdsl] Error 1 make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[5]: *** [CMakeFiles/Makefile2:397: CMakeFiles/uninstall-sdsl.dir/all] Error 2 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[4]: *** [CMakeFiles/Makefile2:404: CMakeFiles/uninstall-sdsl.dir/rule] Error 2 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: *** [Makefile:172: uninstall-sdsl] Error 2 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' 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 -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 -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 -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 -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 -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 -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' 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+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/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 rm -Rf include/google/protobuf deps/protobuf WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. if [ ! -d obj ]; then mkdir -p obj; 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" 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/* if [ ! -d lib ]; then mkdir -p lib; fi touch lib/cleaned_old_protobuf_v003 touch: cannot touch 'lib/cleaned_old_protobuf_v003': No such file or directory find bin obj lib -type f -delete make[2]: *** [Makefile:574: lib/cleaned_old_protobuf_v003] Error 1 make[2]: *** Waiting for unfinished jobs.... 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[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 -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 make[3]: Leaving 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 -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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 -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 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 -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 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 -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 -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 make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; 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 -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 ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/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 -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 if [ ! -d obj ]; then mkdir -p obj; fi 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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/union_find.cpp -o obj/union_find.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 -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 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 -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 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -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 -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 -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 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 -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 -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 -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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -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 -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 -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/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/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/gssw.c: In function ‘gssw_print_graph_cigar’: ./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/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/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_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 /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 | } | ^ 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 C compiler identification is GNU 14.2.0 -- The C compiler identification is GNU 14.2.0 ar rc cuTest.a *.o -- The CXX compiler identification is GNU 14.2.0 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 -- 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 | } | ^ -- Detecting C compiler ABI info -- Detecting C compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting C 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 C compiler ABI info -- 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 CXX compiler ABI info -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compiler ABI info - done -- Detecting C compiler ABI info - 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -pipe -O3 -I. -lm -lz -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting CXX compile features -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting C compile features -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compile features - done -- Detecting CXX compile features - done cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -- Compiler is recent enough to support C++14. -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG libhandlegraph is root project or external_project -- Configuring done (1.6s) -- Configuring done (1.6s) -- 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' 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 -- Generating done (0.1s) -- 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[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' make -f CMakeFiles/Makefile2 all cd C && make 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[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' 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=" 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 cp inc/jsmn.h ../lib/jsmn.h.tmp [ 16%] Building CXX object CMakeFiles/kff.dir/kff_io.cpp.o cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h mv ../lib/jsmn.h.tmp ../lib/jsmn.h mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp 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 mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' 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 [ 5%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o [ 5%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp [ 11%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o [ 17%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h [ 20%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o [ 28%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o [ 34%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o [ 34%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o [ 37%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.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 -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/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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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_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 [ 40%] 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 -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/mutable_path_metadata.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_metadata.cpp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.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 -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_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 [ 42%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o [ 42%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp [ 42%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dfs.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 -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/mutable_path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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/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 /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 -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/serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/serializable.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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 -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 /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 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/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 -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 /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/deletable_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 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-c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp [ 65%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.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 -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_single_stranded.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h [ 68%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h 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 -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 -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 mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o [ 82%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o [ 82%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o [ 82%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.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 -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/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 cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.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 -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 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 -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 mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.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 -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/count_walks.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/count_walks.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 -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 -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 /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 -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 cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o cp inc/sonLibString.h ../lib/sonLibString.h.tmp ar: [ 85%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o creating lib/libstructures.a mv ../lib/sonLibString.h.tmp ../lib/sonLibString.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 -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 cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp [ 88%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.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 -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 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' [ 91%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h src/gssw.c: In function ‘gssw_sw_software_byte’: src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 277 | memcpy(scratch, to_unswizzle, size); | ^ In function ‘unswizzle_byte’, inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: *** [Makefile:622: lib/libstructures.a] Error 1 cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.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 -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 cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS cp inc/stGraph.h ../lib/stGraph.h.tmp [ 94%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o mv ../lib/stGraph.h.tmp ../lib/stGraph.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 -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/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp 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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' ar: /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a: No such file or directory make[2]: *** [Makefile:515: lib/libssw.a] Error 1 -- Performing Test HAVE_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_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- 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. 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); | ^~~~~~~~~~~ -- 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 (4.7s) 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))); | ^ -- 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 -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' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.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/bp_support_algorithm.cpp.o [ 12%] 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 -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 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 -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 [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o [ 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 -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 -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 -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 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 -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 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 -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 [ 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 -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 [ 37%] 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 -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 -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 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 -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 [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.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 -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 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 -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 [ 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 -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 [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o [ 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 -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 -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 [ 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 -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 -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 -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 [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o [ 75%] 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 -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 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 -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 -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 -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 -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 -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 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 -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 -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 [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o [ 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 -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 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 -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 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 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 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' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:637: lib/libsublinearLS.a] Error 1 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 33%] Linking CXX static library libkff.a [ 33%] Built target kff [ 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 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 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o 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' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:598: lib/libgssw.a] Error 1 [ 83%] Linking CXX executable reader_bench 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 &= | ^~~~~ [ 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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Built target kff_example 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 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[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]: 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/depend 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' 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]: Entering 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 [ 97%] Linking CXX shared library libhandlegraph.so make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 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' [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/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 -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' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Built target handlegraph_shared 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); | ^~~~~~~~~~~~ /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 /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=" 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' [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 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: "" CMake Error at cmake_install.cmake:52 (file): file INSTALL destination: /build/reproducible-path/vg-1.59.0+ds/lib is not a directory. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[2]: *** [Makefile:594: lib/libhandlegraph.a] Error 2 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 [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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /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 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/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' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [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" CMake Error at cmake_install.cmake:46 (file): file cannot create directory: /build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig. Maybe need administrative privileges. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' ERROR: Installation failed. make[2]: *** [Makefile:511: lib/libsdsl.a] Error 1 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+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 -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 -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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest 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' cp: cannot stat '/build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a': Not a directory make[2]: *** [Makefile:616: lib/libsonlib.a] Error 1 make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_build: error: make -j42 "INSTALL=install --strip-program=true" SFX=-sse3 all test/build_graph bin/shuf returned exit code 2 make[1]: *** [debian/rules:41: override_dh_auto_build-arch] Error 25 make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' make: *** [debian/rules:22: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3414070 and its subdirectories Starting cleanup. All cleanup done. Tue Feb 10 18:25:43 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-pr64cHEE, removing. /srv/reproducible-results/rbuild-debian/r-b-build.oaKNW60N: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Jan 8 12:02 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jan 8 11:48 b2 -rw------- 1 jenkins jenkins 3936 Jan 8 11:48 rbuildlog.JT8T9J5 -rw-r--r-- 1 jenkins jenkins 2839 Nov 24 12:24 vg_1.59.0+ds-0.1.dsc /srv/reproducible-results/rbuild-debian/r-b-build.oaKNW60N/b1: total 904 -rw-r--r-- 1 jenkins jenkins 924001 Jan 8 12:02 build.log /srv/reproducible-results/rbuild-debian/r-b-build.oaKNW60N/b2: total 0 Wed Jan 8 12:02:43 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Feb 10 06:11:31 -12 2026 I: pbuilder-time-stamp: 1770747091 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 dpkg-source: warning: cannot verify inline signature for ./vg_1.59.0+ds-0.1.dsc: unsupported subcommand 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/3414070/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='41f08ad8ee80430d9397ef020d85867e' 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='3414070' 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.oaKNW60N/pbuilderrc_tYfy --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.oaKNW60N/b1 --logfile b1/build.log vg_1.59.0+ds-0.1.dsc' SUDO_GID='110' SUDO_UID='105' 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 ionos5-amd64 6.11.10+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1~bpo12+1 (2024-12-19) 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/3414070/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 ... 19848 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} libffi8{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} libgcrypt20{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} libgnutls30t64{a} libgpg-error0{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} libidn2-0{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} libonig5{a} libosp5{a} libp11-kit-dev{a} libp11-kit0{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{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} libpython3.13-minimal{a} libpython3.13-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{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} libunistring5{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} libxxhash-dev{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} python3.13{a} python3.13-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 libgpg-error-l10n 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, 390 newly installed, 0 to remove and 0 not upgraded. Need to get 269 MB of archives. After unpacking 1102 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 flex amd64 2.6.4-8.2+b4 [423 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [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 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0046 [41.1 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libdebuginfod-common all 0.192-4 [23.7 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.1-3 [858 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.1-3 [2202 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.1-1 [27.0 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-4 [256 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.1-3 [1973 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.1-3 [740 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.1-1 [9912 B] Get: 24 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.1-1 [28.0 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.4.0-2 [1422 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20241223 [164 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-4 [200 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-14 [92.1 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-4 [723 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 bc amd64 1.07.1-4 [103 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 bison amd64 2:3.8.2+dfsg-1+b2 [1170 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 bwa amd64 0.7.18-1 [212 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.31.3-1 [2268 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 53 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.19.0-3+b3 [49.5 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.8-2 [1454 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.19+dfsg-1 [187 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.1-1 [351 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.31.3-1 [11.9 MB] Get: 72 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.23 [90.6 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 79 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-4 [1600 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.23 [919 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 docbook all 4.5-11 [126 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libosp5 amd64 1.5.2-15.1 [973 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 opensp amd64 1.5.2-15.1 [448 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 docbook-to-man amd64 1:2.0.0-47 [73.6 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 docbook-xml all 4.5-13 [77.4 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 docbook-xsl all 1.79.2+dfsg-7 [1221 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.6-1+b1 [26.0 MB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libclang-cpp19 amd64 1:19.1.6-1+b1 [13.2 MB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libclang1-19 amd64 1:19.1.6-1+b1 [7614 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libfmt10 amd64 10.1.1+ds1-4 [127 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 doxygen amd64 1.9.8+ds-2+b3 [5011 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libdw1t64 amd64 0.192-4 [255 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libasm1t64 amd64 0.192-4 [28.4 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.11.1-1 [360 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libjson-c5 amd64 0.18+ds-1 [46.0 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libdebuginfod1t64 amd64 0.192-4 [32.4 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 elfutils amd64 0.192-4 [505 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-4+b2 [4908 B] Get: 110 http://deb.debian.org/debian unstable/main amd64 libfastahack0 amd64 1.0.0+dfsg-11+b2 [26.4 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 fastahack amd64 1.0.0+dfsg-11+b2 [12.7 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.44-3 [280 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 native-architecture all 0.2.3 [2108 B] Get: 120 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.82.4-1 [1501 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libgirepository-2.0-0 amd64 2.82.4-1 [139 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 girepository-tools amd64 2.82.4-1 [145 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libann0 amd64 1.1.2+doc-9+b1 [25.1 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libcdt5 amd64 2.42.4-2+b2 [40.5 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libcgraph6 amd64 2.42.4-2+b2 [64.3 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.11.0-1 [1879 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.0-1+b1 [550 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libgav1-1 amd64 0.19.0-3 [350 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 librav1e0.7 amd64 0.7.1-9 [939 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1899.20250103-1 [173 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.1.1-1 [117 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-dav1d amd64 1.19.5-1 [11.2 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libde265-0 amd64 1.0.15-1+b2 [189 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-libde265 amd64 1.19.5-1 [15.2 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libheif1 amd64 1.19.5-1 [514 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.1.0-2 [478 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b3 [56.2 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libgd3 amd64 2.3.3-12+b1 [126 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libgts-0.7-5t64 amd64 0.7.6+darcs121130-5.2+b1 [160 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b3 [27.8 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.5.4-2 [415 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.55.0+ds-3 [225 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.55.0+ds-3 [54.6 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.55.0+ds-3 [35.4 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libpathplan4 amd64 2.42.4-2+b2 [42.8 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libgvc6 amd64 2.42.4-2+b2 [685 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libgvpr2 amd64 2.42.4-2+b2 [193 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 liblab-gamut1 amd64 2.42.4-2+b2 [198 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-3+b4 [59.0 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libxaw7 amd64 2:1.0.16-1 [212 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 graphviz amd64 2.42.4-2+b2 [618 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 libgpg-error0 amd64 1.51-3 [82.2 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 5.3.0-1+b1 [1676 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 195 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 xsltproc amd64 1.1.35-1.1+b1 [115 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 gtk-doc-tools all 1.34.0-2 [328 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-5+b1 [210 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libonig5 amd64 6.9.9-1+b1 [189 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libjq1 amd64 1.7.1-3+b1 [164 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 jq amd64 1.7.1-3+b1 [77.8 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-3 [59.5 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-3 [41.7 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-3 [42.0 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-3 [53.5 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-3 [126 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 libbackward-cpp-dev all 1.6-1 [34.3 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 uuid-dev amd64 2.40.2-14 [47.5 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 libblkid-dev amd64 2.40.2-14 [205 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-4 [10.6 MB] Get: 215 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83.0 amd64 1.83.0-4 [347 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83-dev amd64 1.83.0-4 [375 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Get: 218 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 liblzo2-2 amd64 2.10-3+b1 [55.1 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 libcairo-script-interpreter2 amd64 1.18.2-2 [58.8 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 libpng-dev amd64 1.6.44-3 [366 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 libfreetype-dev amd64 2.13.3+dfsg-1 [622 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 libfontconfig-dev amd64 2.15.0-1.1+b1 [414 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 libffi-dev amd64 3.4.6-1 [60.6 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 libsepol-dev amd64 3.7-1 [370 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.44-5 [260 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 libpcre2-32-0 amd64 10.44-5 [248 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 libpcre2-posix3 amd64 10.44-5 [60.4 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 libpcre2-dev amd64 10.44-5 [790 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 libselinux1-dev amd64 3.7-3+b1 [160 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 libmount-dev amd64 2.40.2-14 [29.3 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 libsysprof-capture-4-dev amd64 47.2-1 [47.7 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 libgio-2.0-dev amd64 2.82.4-1 [1678 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 libglib2.0-data all 2.82.4-1 [1276 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 libglib2.0-bin amd64 2.82.4-1 [127 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 libgio-2.0-dev-bin amd64 2.82.4-1 [163 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 libglib2.0-dev-bin amd64 2.82.4-1 [52.0 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 libglib2.0-dev amd64 2.82.4-1 [52.7 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 libpixman-1-dev amd64 0.44.0-3 [11.4 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 x11proto-dev all 2024.1-1 [603 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 x11proto-core-dev all 2024.1-1 [3312 B] Get: 248 http://deb.debian.org/debian unstable/main amd64 libice-dev amd64 2:1.1.1-1 [73.8 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 libsm-dev amd64 2:1.2.4-1 [37.7 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 libxau-dev amd64 1:1.0.11-1 [23.6 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 libxdmcp-dev amd64 1:1.1.5-1 [44.3 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 libxcb1-dev amd64 1.17.0-2+b1 [181 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 libx11-dev amd64 2:1.8.10-2 [891 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 libxcb-render0-dev amd64 1.17.0-2+b1 [118 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0-dev amd64 1.17.0-2+b1 [108 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 libxext-dev amd64 2:1.3.4-1+b3 [104 kB] Get: 258 http://deb.debian.org/debian unstable/main amd64 libxrender-dev amd64 1:0.9.10-1.1+b3 [35.9 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 libcairo2-dev amd64 1.18.2-2 [43.0 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.8-2 [449 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.8-2 [449 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.19.0-3+b3 [98.9 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10-1+b1 [1317 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.8-2 [1391 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-3 [15.7 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.5.19+dfsg-1 [303 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.6.0-2 [88.5 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.9.1-1 [23.1 kB] Get: 276 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.9.1-1 [167 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.4.0-2 [2790 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.11.1-1 [474 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.22-1 [55.8 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 libdisorder-dev amd64 0.0.2+git20130809.8062ee1-4+b2 [4912 B] Get: 285 http://deb.debian.org/debian unstable/main amd64 libdivsufsort3 amd64 2.0.1-6+b1 [45.9 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 libdivsufsort-dev amd64 2.0.1-6+b1 [19.1 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 libelf-dev amd64 0.192-4 [93.2 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 libdw-dev amd64 0.192-4 [335 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 libfastahack-dev amd64 1.0.0+dfsg-11+b2 [27.9 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 libfml0 amd64 0.1+git20221215.85f159e-1 [70.1 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 libfml-dev amd64 0.1+git20221215.85f159e-1 [82.0 kB] Get: 293 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-12 [836 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get: 296 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.20+ds-2 [1701 kB] Get: 297 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-5+b1 [10.4 MB] Get: 298 http://deb.debian.org/debian unstable/main amd64 libjansson-dev amd64 2.14-2+b3 [43.2 kB] Get: 299 http://deb.debian.org/debian unstable/main amd64 libjemalloc2 amd64 5.3.0-2+b2 [275 kB] Get: 300 http://deb.debian.org/debian unstable/main amd64 libjemalloc-dev amd64 5.3.0-2+b2 [491 kB] Get: 301 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get: 302 http://deb.debian.org/debian unstable/main amd64 libxxhash-dev amd64 0.8.3-2 [81.0 kB] Get: 303 http://deb.debian.org/debian unstable/main amd64 liblz4-dev amd64 1.9.4-4 [83.0 kB] Get: 304 http://deb.debian.org/debian unstable/main amd64 libmhash2 amd64 0.9.9.9-10 [92.4 kB] Get: 305 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get: 306 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5-2+b1 [351 kB] Get: 307 http://deb.debian.org/debian unstable/main amd64 libpaper2 amd64 2.2.5-0.3 [16.3 kB] Get: 308 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 2.2.5-0.3 [16.1 kB] Get: 309 http://deb.debian.org/debian unstable/main amd64 libprotobuf32t64 amd64 3.21.12-10+b2 [982 kB] Get: 310 http://deb.debian.org/debian unstable/main amd64 libprotobuf-lite32t64 amd64 3.21.12-10+b2 [274 kB] Get: 311 http://deb.debian.org/debian unstable/main amd64 libprotobuf-dev amd64 3.21.12-10+b2 [1331 kB] Get: 312 http://deb.debian.org/debian unstable/main amd64 libprotoc32t64 amd64 3.21.12-10+b2 [921 kB] Get: 313 http://deb.debian.org/debian unstable/main amd64 libprotoc-dev amd64 3.21.12-10+b2 [1024 kB] Get: 314 http://deb.debian.org/debian unstable/main amd64 libyajl2 amd64 2.1.0-5+b2 [23.3 kB] Get: 315 http://deb.debian.org/debian unstable/main amd64 libraptor2-0 amd64 2.0.16-4+b1 [177 kB] Get: 316 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [795 kB] Get: 317 http://deb.debian.org/debian unstable/main amd64 libxslt1-dev amd64 1.1.35-1.1+b1 [346 kB] Get: 318 http://deb.debian.org/debian unstable/main amd64 libyajl-dev amd64 2.1.0-5+b2 [32.0 kB] Get: 319 http://deb.debian.org/debian unstable/main amd64 libraptor2-dev amd64 2.0.16-4+b1 [211 kB] Get: 320 http://deb.debian.org/debian unstable/main amd64 librasqal3t64 amd64 0.9.33-2.1+b2 [191 kB] Get: 321 http://deb.debian.org/debian unstable/main amd64 librasqal3-dev amd64 0.9.33-2.1+b2 [227 kB] Get: 322 http://deb.debian.org/debian unstable/main amd64 librdf0t64 amd64 1.0.17-4+b1 [107 kB] Get: 323 http://deb.debian.org/debian unstable/main amd64 librdf0-dev amd64 1.0.17-4+b1 [238 kB] Get: 324 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.2-2 [467 kB] Get: 325 http://deb.debian.org/debian unstable/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12+b2 [36.8 kB] Get: 326 http://deb.debian.org/debian unstable/main amd64 libsmithwaterman-dev amd64 0.0+git20160702.2610e25-12+b2 [41.4 kB] Get: 327 http://deb.debian.org/debian unstable/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 328 http://deb.debian.org/debian unstable/main amd64 libssw0 amd64 1.1-15+b2 [21.8 kB] Get: 329 http://deb.debian.org/debian unstable/main amd64 libssw-dev amd64 1.1-15+b2 [24.6 kB] Get: 330 http://deb.debian.org/debian unstable/main amd64 libtabixpp0t64 amd64 1.1.2-2.1+b1 [10.3 kB] Get: 331 http://deb.debian.org/debian unstable/main amd64 libtabixpp-dev amd64 1.1.2-2.1+b1 [9528 B] Get: 332 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get: 333 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 334 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 335 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b3 [54.6 kB] Get: 336 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 337 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get: 338 http://deb.debian.org/debian unstable/main amd64 libtsl-hopscotch-map-dev all 2.3.1-1 [36.6 kB] Get: 339 http://deb.debian.org/debian unstable/main amd64 libwfa2-0 amd64 2.3.3-4+b1 [61.1 kB] Get: 340 http://deb.debian.org/debian unstable/main amd64 libvcflib2 amd64 1.0.9+dfsg1-3+b2 [194 kB] Get: 341 http://deb.debian.org/debian unstable/main amd64 libwfa2-dev amd64 2.3.3-4+b1 [79.7 kB] Get: 342 http://deb.debian.org/debian unstable/main amd64 libvcflib-dev amd64 1.0.9+dfsg1-3+b2 [77.8 kB] Get: 343 http://deb.debian.org/debian unstable/main amd64 zip amd64 3.0-14 [233 kB] Get: 344 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB] Get: 345 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 346 http://deb.debian.org/debian unstable/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Get: 347 http://deb.debian.org/debian unstable/main amd64 r-cran-littler amd64 0.3.20-2 [103 kB] Get: 348 http://deb.debian.org/debian unstable/main amd64 littler all 0.3.20-2 [16.0 kB] Get: 349 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get: 350 http://deb.debian.org/debian unstable/main amd64 r-cran-rcpp amd64 1.0.13-1-1 [2074 kB] Get: 351 http://deb.debian.org/debian unstable/main amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] Get: 352 http://deb.debian.org/debian unstable/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB] Get: 353 http://deb.debian.org/debian unstable/main amd64 r-cran-glue amd64 1.8.0-1 [165 kB] Get: 354 http://deb.debian.org/debian unstable/main amd64 r-cran-rlang amd64 1.1.4-1 [1712 kB] Get: 355 http://deb.debian.org/debian unstable/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get: 356 http://deb.debian.org/debian unstable/main amd64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Get: 357 http://deb.debian.org/debian unstable/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get: 358 http://deb.debian.org/debian unstable/main amd64 r-cran-mass amd64 7.3-64-1 [1113 kB] Get: 359 http://deb.debian.org/debian unstable/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get: 360 http://deb.debian.org/debian unstable/main amd64 r-cran-nlme amd64 3.1.166-1 [2330 kB] Get: 361 http://deb.debian.org/debian unstable/main amd64 r-cran-matrix amd64 1.7-1-1 [4138 kB] Get: 362 http://deb.debian.org/debian unstable/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get: 363 http://deb.debian.org/debian unstable/main amd64 r-cran-farver amd64 2.1.2-1 [1411 kB] Get: 364 http://deb.debian.org/debian unstable/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get: 365 http://deb.debian.org/debian unstable/main amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1716 kB] Get: 366 http://deb.debian.org/debian unstable/main amd64 r-cran-munsell all 0.5.1-1 [237 kB] Get: 367 http://deb.debian.org/debian unstable/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get: 368 http://deb.debian.org/debian unstable/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get: 369 http://deb.debian.org/debian unstable/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get: 370 http://deb.debian.org/debian unstable/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get: 371 http://deb.debian.org/debian unstable/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get: 372 http://deb.debian.org/debian unstable/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get: 373 http://deb.debian.org/debian unstable/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get: 374 http://deb.debian.org/debian unstable/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get: 375 http://deb.debian.org/debian unstable/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get: 376 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 377 http://deb.debian.org/debian unstable/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get: 378 http://deb.debian.org/debian unstable/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get: 379 http://deb.debian.org/debian unstable/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get: 380 http://deb.debian.org/debian unstable/main amd64 r-cran-gridbase all 0.4-7-5 [163 kB] Get: 381 http://deb.debian.org/debian unstable/main amd64 libvcflib-tools amd64 1.0.9+dfsg1-3+b2 [660 kB] Get: 382 http://deb.debian.org/debian unstable/main amd64 protobuf-compiler amd64 3.21.12-10+b2 [84.8 kB] Get: 383 http://deb.debian.org/debian unstable/main amd64 pv amd64 1.9.25-1 [105 kB] Get: 384 http://deb.debian.org/debian unstable/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Get: 385 http://deb.debian.org/debian unstable/main amd64 raptor2-utils amd64 2.0.16-4+b1 [35.0 kB] Get: 386 http://deb.debian.org/debian unstable/main amd64 rasqal-utils amd64 0.9.33-2.1+b2 [43.8 kB] Get: 387 http://deb.debian.org/debian unstable/main amd64 rs amd64 20200313-1 [15.5 kB] Get: 388 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.20-3 [653 kB] Get: 389 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.20+ds-2 [486 kB] Get: 390 http://deb.debian.org/debian unstable/main amd64 xxd amd64 2:9.1.0967-1+b1 [98.7 kB] Fetched 269 MB in 8s (33.4 MB/s) Preconfiguring packages ... 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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 ... 20073 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 libproc2-0:amd64. Preparing to unpack .../1-libproc2-0_2%3a4.0.4-6_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-6) ... 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(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 ... 20858 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.1-1_amd64.deb ... Unpacking python3-minimal (3.13.1-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... 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(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 ... 21836 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.1-1_amd64.deb ... Unpacking python3 (3.13.1-1) ... 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 openssl. Preparing to unpack .../002-openssl_3.4.0-2_amd64.deb ... Unpacking openssl (3.4.0-2) ... 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Selecting previously unselected package libxml2:amd64. Preparing to unpack .../022-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package libarchive13t64:amd64. Preparing to unpack .../023-libarchive13t64_3.7.4-1.1_amd64.deb ... Unpacking libarchive13t64:amd64 (3.7.4-1.1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../024-libbrotli1_1.1.0-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b6) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../025-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../026-libcom-err2_1.47.2-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../027-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../028-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../029-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 .../030-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../031-libunistring5_1.3-1_amd64.deb ... Unpacking libunistring5:amd64 (1.3-1) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../032-libidn2-0_2.3.7-2+b1_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.7-2+b1) ... Selecting previously unselected package libp11-kit0:amd64. 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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 libxft2:amd64. Preparing to unpack .../311-libxft2_2.3.6-1+b3_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b3) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../312-libxss1_1%3a1.2.3-1+b3_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1+b3) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../313-libtk8.6_8.6.15-1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.15-1) ... Selecting previously unselected package libtsl-hopscotch-map-dev. Preparing to unpack .../314-libtsl-hopscotch-map-dev_2.3.1-1_all.deb ... Unpacking libtsl-hopscotch-map-dev (2.3.1-1) ... 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Setting up python3-jaraco.functools (4.1.0-1) ... Setting up libxslt1-dev:amd64 (1.1.35-1.1+b1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up libdebuginfod-common (0.192-4) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up libgirepository-2.0-0:amd64 (2.82.4-1) ... 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 (1.55.0+ds-3) ... Setting up python3-typeguard (4.4.1-1) ... Setting up xsltproc (1.1.35-1.1+b1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libx11-dev:amd64 (2:1.8.10-2) ... Setting up libglib2.0-bin (2.82.4-1) ... 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 libldap-2.5-0:amd64 (2.5.19+dfsg-1) ... Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... 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Setting up libgnutls28-dev:amd64 (3.8.8-2) ... Setting up libcairo-script-interpreter2:amd64 (1.18.2-2) ... Setting up libxmu6:amd64 (2:1.1.3-3+b4) ... Setting up girepository-tools:amd64 (2.82.4-1) ... Setting up libcurl4t64:amd64 (8.11.1-1) ... Setting up libkdb5-10t64:amd64 (1.21.3-3) ... Setting up libfontconfig-dev:amd64 (2.15.0-1.1+b1) ... Setting up libcurl3t64-gnutls:amd64 (8.11.1-1) ... Setting up debhelper (13.23) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.9.1-1) ... Setting up libxaw7:amd64 (2:1.0.16-1) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up r-base-core (4.4.2-1) ... Creating config file /etc/R/Renviron with new version Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... 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 cmake (3.31.3-1) ... Setting up libhts3t64:amd64 (1.20+ds-2) ... 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 krb5-multidev:amd64 (1.21.3-3) ... Setting up r-cran-littler (0.3.20-2) ... Setting up libglib2.0-dev-bin (2.82.4-1) ... Setting up r-cran-rcpp (1.0.13-1-1) ... Setting up libdebuginfod1t64:amd64 (0.192-4) ... Setting up r-cran-rlang (1.1.4-1) ... Setting up r-cran-gridbase (0.4-7-5) ... Setting up littler (0.3.20-2) ... Setting up r-cran-withr (3.0.2+dfsg-1) ... Setting up libraptor2-0:amd64 (2.0.16-4+b1) ... Setting up raptor2-utils (2.0.16-4+b1) ... Setting up r-cran-fansi (1.0.5-1) ... Setting up r-cran-mass (7.3-64-1) ... Setting up librasqal3t64:amd64 (0.9.33-2.1+b2) ... Setting up librdf0t64:amd64 (1.0.17-4+b1) ... Setting up r-cran-glue (1.8.0-1) ... Setting up r-cran-cli (3.6.3-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up samtools (1.20-3) ... 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 r-cran-colorspace (2.1-1+dfsg-1) ... Setting up libglib2.0-dev:amd64 (2.82.4-1) ... 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 r-cran-matrix (1.7-1-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up libtabixpp0t64:amd64 (1.1.2-2.1+b1) ... Setting up libcairo2-dev:amd64 (1.18.2-2) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up rasqal-utils (0.9.33-2.1+b2) ... Setting up elfutils (0.192-4) ... 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 (8.11.1-1) ... Setting up libvcflib2:amd64 (1.0.9+dfsg1-3+b2) ... Setting up r-cran-scales (1.3.0-1) ... Setting up libraptor2-dev:amd64 (2.0.16-4+b1) ... 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 librdf0-dev (1.0.17-4+b1) ... Setting up libtabixpp-dev:amd64 (1.1.2-2.1+b1) ... Setting up libvcflib-dev:amd64 (1.0.9+dfsg1-3+b2) ... Setting up libheif-plugin-dav1d:amd64 (1.19.5-1) ... Setting up libheif-plugin-libde265:amd64 (1.19.5-1) ... Setting up libheif1:amd64 (1.19.5-1) ... Setting up libgd3:amd64 (2.3.3-12+b1) ... Setting up libgvc6 (2.42.4-2+b2) ... Setting up graphviz (2.42.4-2+b2) ... Processing triggers for libc-bin (2.40-5) ... 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 (1.34.0-2) ... Processing triggers for ca-certificates (20241223) ... 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 -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 rm -rf ../bin ../lib make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' 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' rm -rf ./obj/*.o rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' 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 -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 -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 -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 -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 -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 -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* 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. cp deps/BBHash/BooPHF.h /build/reproducible-path/vg-1.59.0+ds/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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc cp -r deps/sparsepp/sparsepp include/ make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' rm -Rf include/dynamic.hpp include/dynamic . ./source_me.sh && cp -r deps/mio/include/mio /build/reproducible-path/vg-1.59.0+ds/include/ 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' rm -Rf include/google/protobuf deps/protobuf 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 -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 . ./source_me.sh && cp -r deps/atomic_queue/include/atomic_queue/* /build/reproducible-path/vg-1.59.0+ds/include/ 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/structures' if [ ! -d bin ]; then mkdir -p bin; fi touch lib/cleaned_old_protobuf_v003 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/* 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" && cmake -DCMAKE_VERBOSE_MAKEFILE=ON .. && make cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ . ./source_me.sh && cp -r deps/ips4o/ips4o* /build/reproducible-path/vg-1.59.0+ds/include/ make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make all touch: cannot touch 'lib/cleaned_old_protobuf_v003': No such file or directory cd quicktree_1.1 && make all CC="gcc -std=c99" make[2]: *** [Makefile:574: lib/cleaned_old_protobuf_v003] Error 1 make[2]: *** Waiting for unfinished jobs.... WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' if [ ! -d obj ]; then mkdir -p obj; fi 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/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 -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 -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 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 -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 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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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 -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 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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -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 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 -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 -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 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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -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 find bin obj lib -type f -delete 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 -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 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -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 -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 -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 make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi 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 -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 -- Setting build type to 'Release' as none was specified. if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi 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 tif [ ! -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 he 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 -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 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 -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 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -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 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./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 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 | } | ^ -- The CXX 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 -- Detecting C compiler ABI info -- Detecting C compiler ABI info -- 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 -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - 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 | } | ^ -- 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 -- Detecting CXX compiler ABI info - done -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info - done -- Configuring done (0.9s) -- Generating done (0.0s) -- 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/g++ - skipped -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting CXX compile features -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compile features - done make[3]: Entering directory '/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 libhandlegraph is root project or external_project -- Configuring done (0.9s) src/gssw.c: In function ‘gssw_graph_print’: -- Detecting CXX compiler ABI info - done 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 -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build 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[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 src/gssw.c: In function ‘gssw_print_graph_cigar’: /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 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 [ 16%] Building CXX object CMakeFiles/kff.dir/kff_io.cpp.o -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done make -f CMakeFiles/Makefile2 all src/gssw.c: In function ‘gssw_create_seed_byte’: 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=" 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 Building in Release mode make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -- Configuring done (1.0s) 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/deletable_handle_graph.cpp.o [ 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 -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 /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 -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 [ 14%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o [ 14%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o [ 20%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o [ 20%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o [ 25%] 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 -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 [ 28%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o [ 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp [ 34%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o [ 37%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include 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-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 -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 [ 74%] Building CXX object 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 -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 make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/debug.dir/build.make CMakeFiles/debug.dir/depend 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/debug.dir/DependInfo.cmake "--color=" 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]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS 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 [ 6%] Building CXX object CMakeFiles/debug.dir/debug.cpp.o /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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/debug.dir/debug.cpp.o -MF CMakeFiles/debug.dir/debug.cpp.o.d -o CMakeFiles/debug.dir/debug.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/debug.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' 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 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 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 cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp make -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/depend mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h 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/rle_lz77_v1.dir/DependInfo.cmake "--color=" cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.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 -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 cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h make[5]: Leaving directory '/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' make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/depend 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/rle_lz77_v2.dir/DependInfo.cmake "--color=" 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 [ 12%] Building CXX object CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o /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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -MF CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o.d -o CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/rle_lz77_v1.cpp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o cp inc/sonLibHash.h ../lib/sonLibHash.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 -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 mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/build cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' 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 [ 18%] Building CXX object CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h /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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -MF CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o.d -o CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/rle_lz77_v2.cpp cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success 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 mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp 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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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 make -f CMakeFiles/h0_lz77.dir/build.make CMakeFiles/h0_lz77.dir/depend 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/h0_lz77.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f 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'/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/rle_bwt.dir/DependInfo.cmake "--color=" [ 82%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o make -f CMakeFiles/cw-bwt.dir/build.make CMakeFiles/cw-bwt.dir/depend /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 -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 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/cw-bwt.dir/DependInfo.cmake "--color=" make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.dir/depend [ 85%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o 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 -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 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/benchmark.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/build [ 88%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o 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 -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 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' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 31%] Building CXX object CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o make -f CMakeFiles/wm_string.dir/build.make CMakeFiles/wm_string.dir/depend /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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -MF CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o.d -o CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/rle_bwt.cpp make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 37%] Building CXX object CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o 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=" /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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -MF CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o.d -o CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/cw-bwt.cpp [ 43%] Building CXX object CMakeFiles/benchmark.dir/benchmark.cpp.o /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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/benchmark.dir/benchmark.cpp.o -MF CMakeFiles/benchmark.dir/benchmark.cpp.o.d -o CMakeFiles/benchmark.dir/benchmark.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/benchmark.cpp 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[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/wm_string.dir/build.make CMakeFiles/wm_string.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' -- Performing Test HAVE_CXA_DEMANGLE [ 50%] Building CXX object CMakeFiles/wm_string.dir/wm_string.cpp.o /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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/wm_string.dir/wm_string.cpp.o -MF CMakeFiles/wm_string.dir/wm_string.cpp.o.d -o CMakeFiles/wm_string.dir/wm_string.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/wm_string.cpp make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:622: lib/libstructures.a] Error 1 [ 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 -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 [ 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 -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 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)) { | ^ 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 -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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. -lm -lz -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- 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 -- Looking for C++ include cstdio - found -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -- Configuring done (3.9s) make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' ar: /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a: No such file or directory make[2]: *** [Makefile:515: lib/libssw.a] Error 1 -- Generating done (0.3s) 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))); | ^ -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build src/gssw.c: In function ‘gssw_sw_software_word’: src/gssw.c:1117:5: warning: ‘__builtin_memcpy’ writing between 18446744069414584336 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 1117 | memcpy(scratch, to_unswizzle, size * sizeof(int16_t)); | ^ In function ‘unswizzle_word’, inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/bits.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o [ 12%] 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 -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 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 -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 [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.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 -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 [ 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 -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_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 -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 [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o [ 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 -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 [ 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 -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 -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 [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/io.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 -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 [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.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 -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 [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o [ 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 -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 [ 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 -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 -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 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 -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 [ 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 -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 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 -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 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 -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 [ 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 -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 -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 [ 87%] 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 -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 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 -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 [ 87%] 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 -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 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 -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 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 -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 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 -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 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 -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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 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 [ 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 -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 -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 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/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 -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 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 [ 56%] Linking CXX executable debug /usr/bin/cmake -E cmake_link_script CMakeFiles/debug.dir/link.txt --verbose=1 [ 33%] Built target kff [ 50%] Building CXX object CMakeFiles/kff_example.dir/main.cpp.o [ 66%] Building CXX object benchmarks/CMakeFiles/reader_bench.dir/reader.cpp.o /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 -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 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]: 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 [ 56%] Built target debug 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 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 &= | ^~~~~ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:637: lib/libsublinearLS.a] Error 1 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 83%] Linking CXX executable reader_bench cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 83%] Built target reader_bench 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 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 -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 -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 -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 [100%] Linking CXX executable kff_example [100%] Built target kff_example 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' cp: cannot stat '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:598: lib/libgssw.a] Error 1 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 -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' [ 62%] Built target wm_string cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 68%] Linking CXX executable benchmark /usr/bin/cmake -E cmake_link_script CMakeFiles/benchmark.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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' [ 81%] Linking CXX executable rle_lz77_v2 [ 81%] Linking CXX executable cw-bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/cw-bwt.dir/link.txt --verbose=1 /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v2.dir/link.txt --verbose=1 [ 81%] Built target benchmark 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 -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 /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 -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' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 81%] Built target rle_lz77_v2 [ 81%] Built target cw-bwt 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' [ 87%] 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 [ 93%] Linking CXX executable rle_lz77_v1 /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 -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 /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/DYNAMIC/build' [ 93%] Built target rle_bwt 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 -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' [ 93%] Built target rle_lz77_v1 [ 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' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Linking CXX static library libhandlegraph.a [100%] Linking CXX shared library libhandlegraph.so /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 [100%] Linking CXX executable h0_lz77 /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/cmake -E cmake_link_script CMakeFiles/h0_lz77.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 -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 /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 -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/DYNAMIC/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 h0_lz77 [100%] Built target handlegraph_shared 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[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/ 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 /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 /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' 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 -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' [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: "" CMake Error at cmake_install.cmake:52 (file): file INSTALL destination: /build/reproducible-path/vg-1.59.0+ds/lib is not a directory. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[2]: *** [Makefile:594: lib/libhandlegraph.a] Error 2 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); | ^~~~~~~~~~~~ [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 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 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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 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 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/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" CMake Error at cmake_install.cmake:46 (file): file cannot create directory: /build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig. Maybe need administrative privileges. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' ERROR: Installation failed. make[2]: *** [Makefile:511: lib/libsdsl.a] Error 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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest 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' cp: cannot stat '/build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a': Not a directory make[2]: *** [Makefile:616: lib/libsonlib.a] Error 1 make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_build: error: make -j42 "INSTALL=install --strip-program=true" SFX=-avx2 all test/build_graph bin/shuf returned exit code 2 make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+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 -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 CMake Error at CMakeModules/cmake_uninstall.cmake:2 (MESSAGE): Cannot find install manifest: "/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/install_manifest.txt" make[6]: *** [CMakeFiles/uninstall-sdsl.dir/build.make:73: CMakeFiles/uninstall-sdsl] Error 1 make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[5]: *** [CMakeFiles/Makefile2:397: CMakeFiles/uninstall-sdsl.dir/all] Error 2 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[4]: *** [CMakeFiles/Makefile2:404: CMakeFiles/uninstall-sdsl.dir/rule] Error 2 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: *** [Makefile:172: uninstall-sdsl] Error 2 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' 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 -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 -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 -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* 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 -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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc . ./source_me.sh && cp deps/mmmultimap/src/mmmultimap.hpp deps/mmmultimap/src/mmmultiset.hpp /build/reproducible-path/vg-1.59.0+ds/include/ cd ./deps/lru_cache && cp *.h* /build/reproducible-path/vg-1.59.0+ds/include/ make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' cp deps/sha1/*.h* /build/reproducible-path/vg-1.59.0+ds/include/ Library will be installed in '/build/reproducible-path/vg-1.59.0+ds' rm -Rf include/google/protobuf deps/protobuf cp deps/progress_bar/progress_bar.hpp /build/reproducible-path/vg-1.59.0+ds/include make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd externalTools && make all 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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+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 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/* if [ ! -d obj ]; then mkdir -p obj; fi make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make all WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. cd quicktree_1.1 && make all CC="gcc -std=c99" touch lib/cleaned_old_protobuf_v003 if [ ! -d lib ]; then mkdir -p lib; fi touch: cannot touch 'lib/cleaned_old_protobuf_v003': No such file or directory 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[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 -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 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 -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' 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 -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 make[2]: *** [Makefile:574: lib/cleaned_old_protobuf_v003] Error 1 make[2]: *** Waiting for unfinished jobs.... 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 -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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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 -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 -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 -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 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[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -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 if [ ! -d obj ]; then mkdir -p obj; fi 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 -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 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/union_find.cpp -o obj/union_find.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 -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 -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 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/stable_double.cpp -o obj/stable_double.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 -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 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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 /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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 ./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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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 C 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 | } | ^ 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/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’: 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 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 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 CXX compiler identification is GNU 14.2.0 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 -- Detecting C compiler ABI info - done -- Detecting C compiler ABI info - 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 -- Check for working C compiler: /usr/bin/gcc - skipped make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' -- Detecting C compile features -- Detecting C compile features - done 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 mv ../lib/avl.h.tmp ../lib/avl.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h mv ../lib/commonC.h.tmp ../lib/commonC.h mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/jsmn.h ../lib/jsmn.h.tmp cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h 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 cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.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/sonLibRandom.h.tmp ../lib/sonLibRandom.h mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stJson.h ../lib/stJson.h.tmp cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h 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 cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp 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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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 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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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 -- The C compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:622: lib/libstructures.a] Error 1 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 -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++ 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 CXX compiler ABI info - done -- Detecting CXX compiler ABI info - done -- Detecting CXX compiler ABI info - done 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 -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting CXX compile features - done libhandlegraph is root project or external_project -- Detecting C compiler ABI info -- Configuring done (2.7s) -- Configuring done (2.7s) -- Generating done (0.0s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build -- 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/kff-cpp-api/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 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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' [ 16%] Building CXX object CMakeFiles/kff.dir/kff_io.cpp.o [ 2%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o [ 5%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o [ 8%] 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 -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 [ 11%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o [ 20%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o [ 17%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o [ 20%] 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 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CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_metadata.cpp [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o [ 28%] 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 -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/deletable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o.d -o 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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 -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 [ 85%] 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 -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 /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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD 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/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/reverse_complement.cpp [ 91%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o [ 94%] 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 -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 /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 -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 /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 -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 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' ar: /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a: No such file or directory make[2]: *** [Makefile:515: lib/libssw.a] Error 1 -- 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 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- 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 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 -- Looking for C++ include cstdio - found -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -- Configuring done (3.8s) -- 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 -f CMakeFiles/Makefile2 sdsl cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 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 [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o [ 25%] 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 -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 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 -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 [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o [ 37%] 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 -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 -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 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 -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 -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 [ 37%] 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 -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 -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 [ 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 -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 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 -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 [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.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 [ 62%] 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 -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 [ 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 -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 [ 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 -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 -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 -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 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 -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 [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.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 -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 [ 75%] 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 -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 [ 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 -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 -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 -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 [ 75%] 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 -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 -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 [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o [ 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 -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 [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.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 -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 -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 -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 -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 -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 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 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 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/sublinear-Li-Stephens' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:637: lib/libsublinearLS.a] Error 1 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 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 -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 -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 -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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 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 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 &= | ^~~~~ [ 33%] Linking CXX static library libkff.a cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 33%] Built target kff cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 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 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:598: lib/libgssw.a] Error 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 [ 83%] Linking CXX executable reader_bench cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Built target kff_example 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 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 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 -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' [ 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 -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' [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[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' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 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: "" CMake Error at cmake_install.cmake:52 (file): file INSTALL destination: /build/reproducible-path/vg-1.59.0+ds/lib is not a directory. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[2]: *** [Makefile:594: lib/libhandlegraph.a] Error 2 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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 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' 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: "Release" CMake Error at cmake_install.cmake:46 (file): file cannot create directory: /build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig. Maybe need administrative privileges. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' ERROR: Installation failed. make[2]: *** [Makefile:511: lib/libsdsl.a] Error 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 -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 -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 -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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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 mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest 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' cp: cannot stat '/build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a': Not a directory make[2]: *** [Makefile:616: lib/libsonlib.a] Error 1 make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_build: error: make -j42 "INSTALL=install --strip-program=true" SFX=-avx all test/build_graph bin/shuf returned exit code 2 make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+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 -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 CMake Error at CMakeModules/cmake_uninstall.cmake:2 (MESSAGE): Cannot find install manifest: "/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/install_manifest.txt" make[6]: *** [CMakeFiles/uninstall-sdsl.dir/build.make:73: CMakeFiles/uninstall-sdsl] Error 1 make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[5]: *** [CMakeFiles/Makefile2:397: CMakeFiles/uninstall-sdsl.dir/all] Error 2 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[4]: *** [CMakeFiles/Makefile2:404: CMakeFiles/uninstall-sdsl.dir/rule] Error 2 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: *** [Makefile:172: uninstall-sdsl] Error 2 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' 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 -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 -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 -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 -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 -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 -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 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 -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/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 -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 rm -Rf include/google/protobuf deps/protobuf 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' touch: cannot touch 'lib/cleaned_old_protobuf_v003': No such file or directory make[2]: *** [Makefile:574: lib/cleaned_old_protobuf_v003] Error 1 make[2]: *** Waiting for unfinished jobs.... 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 -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 make[3]: Leaving 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 -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[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 -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 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c gcc -std=c99 -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 -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 -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 make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; 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 -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 /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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -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 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 -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 if [ ! -d lib ]; then mkdir -p lib; fi 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 -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 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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/stable_double.cpp -o obj/stable_double.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 -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 -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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -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 -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 -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 -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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -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 -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/tree.c: In function ‘read_newhampshire_Tnode’: ./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/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./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: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 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. /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 src/gssw.c: In function ‘gssw_print_graph_cigar’: -- The CXX compiler identification is GNU 14.2.0 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 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info src/gssw.c: In function ‘gssw_create_seed_byte’: -- Detecting C compiler ABI info 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 -- The C compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Check for working C compiler: /usr/bin/gcc - 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 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 CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done (0.6s) libhandlegraph is root project or external_project -- Configuring done (0.6s) -- 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' -- 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=" [ 16%] Building CXX object CMakeFiles/kff.dir/kff_io.cpp.o 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' [ 11%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_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/dfs.cpp.o [ 11%] 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 -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 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 /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 -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/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 [ 14%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_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 -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/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 /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 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-fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/eades_algorithm.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 -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/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 [ 71%] Building CXX object 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 -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/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 -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done [ 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 -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 -- Compiler is recent enough to support C++14. -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG 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' [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' /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 -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 cd C && make all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.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 -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 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 cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h [ 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 -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 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 cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS 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 mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h [ 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 -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 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 mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h [ 88%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.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 -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 [ 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 -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 [ 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 -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 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 -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 -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 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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:622: lib/libstructures.a] Error 1 -- Performing Test HAVE_CXA_DEMANGLE 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 -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++ -- 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 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)) { | ^ -- Looking for C++ include cstdio - found 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' ar: /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a: No such file or directory make[2]: *** [Makefile:515: lib/libssw.a] Error 1 -- Configuring done (2.5s) cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- 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 -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_config.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.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 -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 -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 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 -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 [ 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 -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 [ 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 -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 [ 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 -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 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 -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 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 -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 -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 [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o [ 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 -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 [ 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 -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/io.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o [ 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 -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 [ 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 -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 [ 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 -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/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 -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 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 -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 [ 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 -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 -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 [ 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 -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/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 -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 [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.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 -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 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 -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 -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 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 -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 -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 -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 -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 [ 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 -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 [ 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 -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 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 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 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 33%] Built target kff [ 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 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 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 &= | ^~~~~ [ 83%] Linking CXX executable 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 [ 83%] Built target reader_bench 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' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:637: lib/libsublinearLS.a] Error 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 [100%] Linking CXX executable kff_example # 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 -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 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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%] Built target kff_example 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 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' cp: cannot stat '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:598: lib/libgssw.a] Error 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 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 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]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 97%] Linking CXX static library libhandlegraph.a [100%] Linking CXX shared library libhandlegraph.so /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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /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 -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 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%] 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[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 [ 97%] Built target handlegraph_static 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: "" CMake Error at cmake_install.cmake:52 (file): file INSTALL destination: /build/reproducible-path/vg-1.59.0+ds/lib is not a directory. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[2]: *** [Makefile:594: lib/libhandlegraph.a] Error 2 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 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 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 -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/ /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' 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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm [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=" mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+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" CMake Error at cmake_install.cmake:46 (file): file cannot create directory: /build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig. Maybe need administrative privileges. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' ERROR: Installation failed. make[2]: *** [Makefile:511: lib/libsdsl.a] Error 1 mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest 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' cp: cannot stat '/build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a': Not a directory make[2]: *** [Makefile:616: lib/libsonlib.a] Error 1 make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_build: error: make -j42 "INSTALL=install --strip-program=true" SFX=-sse4.1 all test/build_graph bin/shuf returned exit code 2 make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+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 -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 CMake Error at CMakeModules/cmake_uninstall.cmake:2 (MESSAGE): Cannot find install manifest: "/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/install_manifest.txt" make[6]: *** [CMakeFiles/uninstall-sdsl.dir/build.make:73: CMakeFiles/uninstall-sdsl] Error 1 make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[5]: *** [CMakeFiles/Makefile2:397: CMakeFiles/uninstall-sdsl.dir/all] Error 2 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[4]: *** [CMakeFiles/Makefile2:404: CMakeFiles/uninstall-sdsl.dir/rule] Error 2 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: *** [Makefile:172: uninstall-sdsl] Error 2 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' 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 -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 -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 -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 -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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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 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' 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 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. 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/* 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 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' touch: cannot touch 'lib/cleaned_old_protobuf_v003': No such file or directory make[2]: *** [Makefile:574: lib/cleaned_old_protobuf_v003] Error 1 make[2]: *** Waiting for unfinished jobs.... 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 -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]: 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' 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 -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 -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 -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 -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 -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 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 -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 /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 -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 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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -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 lib ]; then mkdir -p lib; fi 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 -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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.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 -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 -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 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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -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 -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 -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 -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 -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 -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 -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 -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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 C compiler identification is GNU 14.2.0 -- The C compiler identification is GNU 14.2.0 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 /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 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 -- The CXX 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 C compiler ABI info -- Detecting CXX compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compiler ABI info - done ar rc cuTest.a *.o ranlib cuTest.a -- Detecting CXX compiler ABI info - done rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' -- Detecting C compile features - done -- 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 -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- 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 CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting CXX compile features - done -- Detecting C compiler ABI info - done libhandlegraph is root project or external_project -- Configuring done (0.8s) -- Configuring done (0.8s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build -- 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 make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -- Check for working C compiler: /usr/bin/gcc - skipped /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 -- Detecting C compile features -- Detecting C compile features - 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 -- Compiler is recent enough to support C++14. -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG 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" 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object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o [ 17%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_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 -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/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 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' 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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 -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 [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o make[4]: Entering 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/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 -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/is_single_stranded.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_single_stranded.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 -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/count_walks.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/count_walks.cpp [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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/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 -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/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 -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/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 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 [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o cp inc/hashTableC.h ../lib/hashTableC.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 -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/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 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 cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp 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 -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o cp inc/stSafeC.h ../lib/stSafeC.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 -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/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 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 cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -pipe -O3 -I. -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 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 -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/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 [ 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 -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/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 [ 88%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/chop.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 -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/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 [ 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 -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/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 [ 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 -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/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 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 -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++ -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success -- Performing Test HAVE_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)) { | ^ 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' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:622: lib/libstructures.a] Error 1 src/gssw.c: In function ‘gssw_sw_software_byte’: src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 277 | memcpy(scratch, to_unswizzle, size); | ^ In function ‘unswizzle_byte’, inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' ar: /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a: No such file or directory make[2]: *** [Makefile:515: lib/libssw.a] Error 1 -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- 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 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Looking for C++ include cstdio - found -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -- Configuring done (3.8s) 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))); | ^ -- 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' [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o [ 37%] 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 -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 [ 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 -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 -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 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 -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 -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 -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 -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 [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/io.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 -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 [ 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 -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 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 -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 [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o [ 62%] 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 -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 -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 [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o [ 75%] 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 -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 [ 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 -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 -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 [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.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 -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 [ 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 -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 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 -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 -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 [ 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 -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 [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o [ 87%] 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 -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 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 -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 [ 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 -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 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 -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 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 -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 -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 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 -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 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 -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 -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 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 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 [ 33%] Linking CXX static library libkff.a 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 [ 33%] Built target kff 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/sublinear-Li-Stephens' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:637: lib/libsublinearLS.a] Error 1 [ 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); | ^~~~~~~~~~ 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 -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 -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 -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 [ 83%] Built target 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[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:598: lib/libgssw.a] Error 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 [100%] Linking CXX executable kff_example cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Built target kff_example 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' [ 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' [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 /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 -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_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 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' 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); | ^~~~~~~~~~~~ [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=" 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' 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' [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 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: "" CMake Error at cmake_install.cmake:52 (file): file INSTALL destination: /build/reproducible-path/vg-1.59.0+ds/lib is not a directory. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[2]: *** [Makefile:594: lib/libhandlegraph.a] Error 2 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 [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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /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*' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 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 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/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" CMake Error at cmake_install.cmake:46 (file): file cannot create directory: /build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig. Maybe need administrative privileges. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' ERROR: Installation failed. make[2]: *** [Makefile:511: lib/libsdsl.a] Error 1 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 -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 -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 -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 -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 -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 mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest 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' cp: cannot stat '/build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a': Not a directory make[2]: *** [Makefile:616: lib/libsonlib.a] Error 1 make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_build: error: make -j42 "INSTALL=install --strip-program=true" SFX=-ssse3 all test/build_graph bin/shuf returned exit code 2 make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+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 -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 CMake Error at CMakeModules/cmake_uninstall.cmake:2 (MESSAGE): Cannot find install manifest: "/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/install_manifest.txt" make[6]: *** [CMakeFiles/uninstall-sdsl.dir/build.make:73: CMakeFiles/uninstall-sdsl] Error 1 make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[5]: *** [CMakeFiles/Makefile2:397: CMakeFiles/uninstall-sdsl.dir/all] Error 2 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[4]: *** [CMakeFiles/Makefile2:404: CMakeFiles/uninstall-sdsl.dir/rule] Error 2 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: *** [Makefile:172: uninstall-sdsl] Error 2 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' 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 -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 -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 -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 -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 -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 -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' 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+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/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 rm -Rf include/google/protobuf deps/protobuf WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. if [ ! -d obj ]; then mkdir -p obj; 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" 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/* if [ ! -d lib ]; then mkdir -p lib; fi touch lib/cleaned_old_protobuf_v003 touch: cannot touch 'lib/cleaned_old_protobuf_v003': No such file or directory find bin obj lib -type f -delete make[2]: *** [Makefile:574: lib/cleaned_old_protobuf_v003] Error 1 make[2]: *** Waiting for unfinished jobs.... 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[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 -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 make[3]: Leaving 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 -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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 -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 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 -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 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 -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 -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 make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; 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 -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 ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/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 -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 if [ ! -d obj ]; then mkdir -p obj; fi 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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/union_find.cpp -o obj/union_find.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 -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 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 -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 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 -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 -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 -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 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 -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 -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 -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 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -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 -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 -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/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/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/gssw.c: In function ‘gssw_print_graph_cigar’: ./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/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/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_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 /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 | } | ^ 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 C compiler identification is GNU 14.2.0 -- The C compiler identification is GNU 14.2.0 ar rc cuTest.a *.o -- The CXX compiler identification is GNU 14.2.0 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 -- 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 | } | ^ -- Detecting C compiler ABI info -- Detecting C compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting C 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 C compiler ABI info -- 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 CXX compiler ABI info -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compiler ABI info - done -- Detecting C compiler ABI info - 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -pipe -O3 -I. -lm -lz -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting CXX compile features -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting C compile features -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compile features - done -- Detecting CXX compile features - done cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -- Compiler is recent enough to support C++14. -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG libhandlegraph is root project or external_project -- Configuring done (1.6s) -- Configuring done (1.6s) -- 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' 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 -- Generating done (0.1s) -- 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[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' make -f CMakeFiles/Makefile2 all cd C && make 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[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' 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=" 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 cp inc/jsmn.h ../lib/jsmn.h.tmp [ 16%] Building CXX object CMakeFiles/kff.dir/kff_io.cpp.o cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h mv ../lib/jsmn.h.tmp ../lib/jsmn.h mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp 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 mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' 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 [ 5%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o [ 5%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp [ 11%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o [ 17%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h [ 20%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o [ 28%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o [ 34%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o [ 34%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o [ 37%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.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 -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/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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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_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 [ 40%] 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 -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/mutable_path_metadata.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_metadata.cpp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.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 -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_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 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/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 -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 /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/deletable_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 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CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o [ 82%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o [ 82%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o [ 82%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.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 -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/dijkstra.cpp.o -MF 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/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/append_graph.cpp 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 -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 mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.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 -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/count_walks.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/count_walks.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 -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 -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 /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 -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 cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o cp inc/sonLibString.h ../lib/sonLibString.h.tmp ar: [ 85%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o creating lib/libstructures.a mv ../lib/sonLibString.h.tmp ../lib/sonLibString.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 -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 cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp [ 88%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.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 -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 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' [ 91%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h src/gssw.c: In function ‘gssw_sw_software_byte’: src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 277 | memcpy(scratch, to_unswizzle, size); | ^ In function ‘unswizzle_byte’, inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: *** [Makefile:622: lib/libstructures.a] Error 1 cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.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 -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 cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS cp inc/stGraph.h ../lib/stGraph.h.tmp [ 94%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o mv ../lib/stGraph.h.tmp ../lib/stGraph.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 -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/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp 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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' ar: /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a: No such file or directory make[2]: *** [Makefile:515: lib/libssw.a] Error 1 -- Performing Test HAVE_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_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- 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. 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); | ^~~~~~~~~~~ -- 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 (4.7s) 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))); | ^ -- 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 -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' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.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/bp_support_algorithm.cpp.o [ 12%] 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 -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 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 -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 [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o [ 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 -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 -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 -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 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 -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 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 -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 [ 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 -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 [ 37%] 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 -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 -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 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 -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 [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.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 -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 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 -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 [ 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 -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 [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o [ 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 -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 -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 [ 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 -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 -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 -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 [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o [ 75%] 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 -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 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 -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 -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 -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 -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 -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 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 -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 -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 [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o [ 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 -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 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 -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 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 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 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' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:637: lib/libsublinearLS.a] Error 1 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 33%] Linking CXX static library libkff.a [ 33%] Built target kff [ 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 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 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o 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' cp: cannot create regular file '/build/reproducible-path/vg-1.59.0+ds/lib/': Not a directory make[2]: *** [Makefile:598: lib/libgssw.a] Error 1 [ 83%] Linking CXX executable reader_bench 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 &= | ^~~~~ [ 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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Built target kff_example 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 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[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]: 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/depend 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' 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]: Entering 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 [ 97%] Linking CXX shared library libhandlegraph.so make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 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' [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/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 -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' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Built target handlegraph_shared 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); | ^~~~~~~~~~~~ /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 /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=" 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' [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 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: "" CMake Error at cmake_install.cmake:52 (file): file INSTALL destination: /build/reproducible-path/vg-1.59.0+ds/lib is not a directory. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[2]: *** [Makefile:594: lib/libhandlegraph.a] Error 2 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 [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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /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 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/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' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [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" CMake Error at cmake_install.cmake:46 (file): file cannot create directory: /build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig. Maybe need administrative privileges. make[3]: *** [Makefile:103: install] Error 1 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' ERROR: Installation failed. make[2]: *** [Makefile:511: lib/libsdsl.a] Error 1 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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+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 -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 -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 -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 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest 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' cp: cannot stat '/build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a': Not a directory make[2]: *** [Makefile:616: lib/libsonlib.a] Error 1 make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_build: error: make -j42 "INSTALL=install --strip-program=true" SFX=-sse3 all test/build_graph bin/shuf returned exit code 2 make[1]: *** [debian/rules:41: override_dh_auto_build-arch] Error 25 make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' make: *** [debian/rules:22: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3414070 and its subdirectories vg failed to build from source. removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/vg_1.59.0+ds-0.1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/vg_1.59.0+ds-0.1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/vg_1.59.0+ds-0.1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/vg_1.59.0+ds-0.1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/dbd/unstable/amd64/vg_1.59.0+ds-0.1.diffoscope.html' removed '/var/lib/jenkins/userContent/reproducible/debian/dbdtxt/unstable/amd64/vg_1.59.0+ds-0.1.diffoscope.txt.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/dbdjson/unstable/amd64/vg_1.59.0+ds-0.1.diffoscope.json.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/vg_1.59.0+ds-0.1_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/vg_1.59.0+ds-0.1.diff.gz' Wed Jan 8 12:02:44 UTC 2025 W: No second build log, what happened? Compressing the 1st log... b1/build.log: 89.7% -- replaced with stdout Wed Jan 8 12:02:45 UTC 2025 I: https://tests.reproducible-builds.org/debian/unstable/amd64/vg : FTBR ➤ FTBFS INSERT 0 1 INSERT 0 1 DELETE 1 [2025-01-08 12:02:46] INFO: Starting at 2025-01-08 12:02:46.108511 [2025-01-08 12:02:46] INFO: Generating the pages of 1 package(s) [2025-01-08 12:02:46] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/vg didn't produce a buildlog, even though it has been built. [2025-01-08 12:02:46] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/vg_1.59.0+ds-0.1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/vg_1.59.0+ds-0.1.diff.gz is missing [2025-01-08 12:02:46] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/vg_1.59.0+ds-0.1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/vg_1.59.0+ds-0.1.diff.gz is missing [2025-01-08 12:02:46] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/amd64/vg_1.30.0+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/amd64/vg_1.30.0+ds-1.diff.gz is missing [2025-01-08 12:02:46] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/arm64/vg_1.30.0+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/arm64/vg_1.30.0+ds-1.diff.gz is missing [2025-01-08 12:02:46] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/armhf/vg_1.30.0+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/armhf/vg_1.30.0+ds-1.diff.gz is missing [2025-01-08 12:02:46] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/i386/vg_1.30.0+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/i386/vg_1.30.0+ds-1.diff.gz is missing [2025-01-08 12:02:46] INFO: Finished at 2025-01-08 12:02:46.553596, took: 0:00:00.445100 Wed Jan 8 12:02:46 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/vg.html [2025-01-08 12:02:47] INFO: Starting at 2025-01-08 12:02:47.080211 [2025-01-08 12:02:47] INFO: Scheduling packages in amd64/unstable [2025-01-08 12:02:47] INFO: jenkins scheduled in unstable/amd64, reason: 'FTBR ➤ FTBFS': vg [2025-01-08 12:02:47] INFO: Finished at 2025-01-08 12:02:47.865237, took: 0:00:00.785037 Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/vg_1.59.0+ds-0.1.rbuild.log: 89.5% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/vg_1.59.0+ds-0.1.rbuild.log.gz [2025-01-08 12:02:48] INFO: Starting at 2025-01-08 12:02:48.310071 [2025-01-08 12:02:48] INFO: Generating the pages of 1 package(s) [2025-01-08 12:02:48] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/vg_1.59.0+ds-0.1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/vg_1.59.0+ds-0.1.diff.gz is missing [2025-01-08 12:02:48] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/vg_1.59.0+ds-0.1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/vg_1.59.0+ds-0.1.diff.gz is missing [2025-01-08 12:02:48] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/vg_1.59.0+ds-0.1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/vg_1.59.0+ds-0.1.diff.gz is missing [2025-01-08 12:02:48] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/amd64/vg_1.30.0+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/amd64/vg_1.30.0+ds-1.diff.gz is missing [2025-01-08 12:02:48] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/arm64/vg_1.30.0+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/arm64/vg_1.30.0+ds-1.diff.gz is missing [2025-01-08 12:02:48] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/armhf/vg_1.30.0+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/armhf/vg_1.30.0+ds-1.diff.gz is missing [2025-01-08 12:02:48] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/i386/vg_1.30.0+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/i386/vg_1.30.0+ds-1.diff.gz is missing [2025-01-08 12:02:48] INFO: Finished at 2025-01-08 12:02:48.615620, took: 0:00:00.305556 All cleanup done. Wed Jan 8 12:02:48 UTC 2025 - total duration: 0h 14m 35s. Wed Jan 8 12:02:48 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-Y1vrdMlp, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 14min 38.041s CPU time consumed: 7.568s