Diff of the two buildlogs: -- --- b1/build.log 2024-12-16 05:14:29.782737971 +0000 +++ b2/build.log 2024-12-16 05:39:49.045552423 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jan 17 23:18:32 -12 2026 -I: pbuilder-time-stamp: 1768735112 +I: Current time: Mon Dec 16 19:14:39 +14 2024 +I: pbuilder-time-stamp: 1734326079 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -52,52 +52,84 @@ dpkg-source: info: applying python3 I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2636781/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3891550/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 16 05:14 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3891550/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3891550/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='51c40109a29749578de3aee026955615' - 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='2636781' - PS1='# ' - PS2='> ' + INVOCATION_ID=752a04a8547d4c7bbf812c58b495b582 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3891550 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.13mrvSh8/pbuilderrc_R7h5 --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.13mrvSh8/b1 --logfile b1/build.log vg_1.59.0+ds-0.1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.13mrvSh8/pbuilderrc_OFoh --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.13mrvSh8/b2 --logfile b2/build.log vg_1.59.0+ds-0.1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink01-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2636781/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3891550/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -629,7 +661,7 @@ Get: 380 http://deb.debian.org/debian unstable/main arm64 samtools arm64 1.20-3+b1 [629 kB] Get: 381 http://deb.debian.org/debian unstable/main arm64 tabix arm64 1.20+ds-2 [455 kB] Get: 382 http://deb.debian.org/debian unstable/main arm64 xxd arm64 2:9.1.0861-1 [97.7 kB] -Fetched 251 MB in 1s (218 MB/s) +Fetched 251 MB in 1s (224 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package m4. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20082 files and directories currently installed.) @@ -1871,8 +1903,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Jan 18 11:19:23 UTC 2026. -Universal Time is now: Sun Jan 18 11:19:23 UTC 2026. +Local time is now: Mon Dec 16 05:15:33 UTC 2024. +Universal Time is now: Mon Dec 16 05:15:33 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libsysprof-capture-4-dev:arm64 (47.2-1) ... @@ -2220,7 +2252,11 @@ 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 +I: user script /srv/workspace/pbuilder/3891550/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3891550/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/vg-1.59.0+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 @@ -2259,15 +2295,15 @@ 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 +cd quicktree_1.1 && make clean 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/cutest' 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' @@ -2311,51 +2347,22 @@ . ./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/ -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. -. ./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* -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c -cp deps/BBHash/BooPHF.h /build/reproducible-path/vg-1.59.0+ds/include -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' -rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc 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' 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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' -cp -r deps/sparsepp/sparsepp include/ -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 WARNING: .git/hooks directory does not exists. -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/* The pre-commit hook is not installed. -make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' -cd cutest && make all -rm -Rf include/dynamic.hpp include/dynamic -if [ ! -d obj ]; then mkdir -p obj; fi -make[3]: Leaving 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/sublinear-Li-Stephens' -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj; fi -gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c -if [ ! -d lib ]; then mkdir -p lib; fi +. ./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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. +rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc +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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. +cp deps/BBHash/BooPHF.h /build/reproducible-path/vg-1.59.0+ds/include +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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c rm -Rf include/google/protobuf deps/protobuf -# annoyingly doesn't have an install option on the cmake, so we manually move their external dependency headers -find bin obj lib -type f -delete touch lib/cleaned_old_protobuf_v003 -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 -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" && cmake -DCMAKE_VERBOSE_MAKEFILE=ON .. && make -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' -. ./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/structures' -if [ ! -d bin ]; then mkdir -p bin; fi -if [ ! -d obj ]; then mkdir -p obj; fi -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin; fi -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c src/union_find.cpp -o obj/union_find.o +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for 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. @@ -2365,8 +2372,25 @@ to work with policies introduced by or earlier. -. ./source_me.sh && cp -r deps/atomic_queue/include/atomic_queue/* /build/reproducible-path/vg-1.59.0+ds/include/ -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 +cp -r deps/sparsepp/sparsepp include/ +rm -Rf include/dynamic.hpp include/dynamic +# annoyingly doesn't have an install option on the cmake, so we manually move their external dependency headers +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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" && cmake -DCMAKE_VERBOSE_MAKEFILE=ON .. && make +. ./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/sublinear-Li-Stephens' +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' +cd externalTools && make all +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 +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 +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' +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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c +if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj; fi CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. @@ -2377,24 +2401,39 @@ -- Setting build type to 'Release' as none was specified. +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 +-- The C compiler identification is GNU 14.2.0 +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 +-- The C compiler identification is GNU 14.2.0 +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 +find bin obj lib -type f -delete 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' +. ./source_me.sh && cp -r deps/atomic_queue/include/atomic_queue/* /build/reproducible-path/vg-1.59.0+ds/include/ +-- The CXX compiler identification is GNU 14.2.0 +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 +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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c src/union_find.cpp -o obj/union_find.o . ./source_me.sh && cp -r deps/ips4o/ips4o* /build/reproducible-path/vg-1.59.0+ds/include/ -- The C compiler identification is GNU 14.2.0 cd ./deps/lru_cache && cp *.h* /build/reproducible-path/vg-1.59.0+ds/include/ --- The C compiler identification is GNU 14.2.0 +-- The CXX compiler identification is GNU 14.2.0 cp deps/sha1/*.h* /build/reproducible-path/vg-1.59.0+ds/include/ +-- The CXX compiler identification is GNU 14.2.0 cp deps/progress_bar/progress_bar.hpp /build/reproducible-path/vg-1.59.0+ds/include +-- Detecting C compiler ABI info 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/ -- The C compiler identification is GNU 14.2.0 -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o --- The CXX compiler identification is GNU 14.2.0 --- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info +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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o +-- Detecting CXX compiler ABI info -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info src/gssw.c: In function ‘gssw_graph_print’: --- The CXX compiler identification is GNU 14.2.0 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); | ~~~^ ~~~~~ @@ -2442,8 +2481,6 @@ | | uint64_t {aka long unsigned int} | long long unsigned int | %lu -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 --- Detecting C compiler ABI info 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); @@ -2452,7 +2489,6 @@ | | uint64_t {aka long unsigned int} | long long unsigned int | %lu --- The C compiler identification is GNU 14.2.0 src/gssw.c: In function ‘gssw_create_seed_byte’: src/gssw.c:5095:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5095 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); @@ -2462,7 +2498,6 @@ | long long unsigned int | %lu src/gssw.c: In function ‘gssw_create_seed_word’: --- Detecting CXX compiler ABI info src/gssw.c:5130:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5130 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); | ~~~^ ~~~~~~~~~~~ @@ -2470,115 +2505,131 @@ | | uint64_t {aka long unsigned int} | long long unsigned int | %lu +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o +-- Detecting C compiler ABI info - done mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make all CC="gcc -std=c99" 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c --- 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 +-- Detecting C compiler ABI info - done +-- Detecting CXX compiler ABI info - done +-- Detecting C compiler ABI info - done +-- Detecting CXX compiler ABI info -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done --- Detecting C compiler ABI info - done --- Detecting CXX compiler ABI info --- Detecting CXX compiler ABI info -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done --- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting CXX compiler ABI info -- Detecting C compiler ABI info +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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c +-- Detecting CXX compiler ABI info 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c --- Detecting CXX compiler ABI info - done --- Detecting CXX compiler ABI info - done ./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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +-- Detecting CXX compiler ABI info - done ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Check for working CXX compiler: /usr/bin/g++ - skipped +-- Detecting C compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done --- Check for working CXX compiler: /usr/bin/g++ - skipped +-- Detecting CXX compiler ABI info - done +-- Detecting CXX compiler ABI info - done +libhandlegraph is root project or external_project +-- Configuring done (1.2s) +-- Check for working C compiler: /usr/bin/gcc - skipped +-- Detecting C compile features +-- Detecting C compile features - done +-- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -libhandlegraph is root project or external_project --- Configuring done (0.7s) --- Detecting CXX compiler ABI info - done -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --- Configuring done (0.8s) --- Generating done (0.0s) --- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build --- Detecting C compiler ABI info - done make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +-- Compiler is recent enough to support C++14. +-- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG /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 --- Check for working CXX compiler: /usr/bin/c++ - skipped +-- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' --- Detecting CXX compile features - done +Building in Release mode-- Detecting CXX compile features - done + +-- Configuring done (1.2s) +-- Generating done (0.0s) +-- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build +-- Configuring done (1.3s) +-- Generating done (0.0s) +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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c +-- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks +make[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 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 -Building in Release modemake[5]: Entering 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/kff-cpp-api/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_objs.dir/DependInfo.cmake "--color=" --- Check for working C compiler: /usr/bin/gcc - skipped --- Detecting C compile features --- Detecting C compile features - done - --- Configuring done (0.8s) -make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' --- Generating done (0.0s) --- Build files have been written to: /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' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' --- Compiler is recent enough to support C++14. --- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG -make[5]: 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/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 +/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build//CMakeFiles/progress.marks +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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c [ 2%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build//CMakeFiles/progress.marks -[ 16%] Building CXX object CMakeFiles/kff.dir/kff_io.cpp.o make -f CMakeFiles/Makefile2 all +make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/debug.dir/build.make CMakeFiles/debug.dir/depend -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/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' +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c [ 6%] Building CXX object CMakeFiles/debug.dir/debug.cpp.o +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' /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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +[ 16%] Building CXX object CMakeFiles/kff.dir/kff_io.cpp.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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c -gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. -lm -lz 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success +[ 5%] 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +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)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c ./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); @@ -2608,65 +2659,60 @@ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +rm -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' make -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/depend +diff: include/vg_environment_version.hpp: No such file or directory +-- Performing Test HAVE_CXA_DEMANGLE 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=" -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. -lm -lz 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' +. ./source_me.sh && g++ -I -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/progress_bar.o deps/progress_bar/progress_bar.cpp [ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -[ 5%] 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. -lm -lz --- Performing Test HAVE_CXA_DEMANGLE -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' -diff: include/vg_environment_version.hpp: No such file or directory -. ./source_me.sh && g++ -I -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/progress_bar.o deps/progress_bar/progress_bar.cpp -g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp -src/gssw.c: In function ‘gssw_sw_software_byte’: -src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] - 277 | memcpy(scratch, to_unswizzle, size); +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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. -lm -lz +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +src/gssw.c: In function ‘gssw_sw_software_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_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)); +In function ‘unswizzle_word’, + inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: +src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ + 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE --- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success --- Could NOT find Git (missing: GIT_EXECUTABLE) -CMake Warning at CMakeLists.txt:102 (message): - git not found. Cloning of submodules will not work. - - --- Looking for C++ include cstdio -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. -lm -lz -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm -ln -s `which shuf` bin/shuf -. ./source_me.sh && cp deps/mmmultimap/src/mmmultimap.hpp deps/mmmultimap/src/mmmultiset.hpp /build/reproducible-path/vg-1.59.0+ds/include/ 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' -[ 8%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o cp inc/avl.h ../lib/avl.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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 mv ../lib/avl.h.tmp ../lib/avl.h +[ 11%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o cp inc/bioioC.h ../lib/bioioC.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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 mv ../lib/bioioC.h.tmp ../lib/bioioC.h --- Looking for C++ include cstdio - found cp inc/commonC.h ../lib/commonC.h.tmp +ln -s `which shuf` bin/shuf mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h +-- 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 +. ./source_me.sh && cp deps/mmmultimap/src/mmmultimap.hpp deps/mmmultimap/src/mmmultiset.hpp /build/reproducible-path/vg-1.59.0+ds/include/ 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 @@ -2675,13 +2721,26 @@ mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h +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); + | ^~~~~~~~~~~ +[ 14%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' +ar: creating /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a 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 +[ 17%] 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h @@ -2691,132 +2750,33 @@ mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h +-- Looking for C++ include cstdio - found 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 -[ 11%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp +-- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp +[ 20%] 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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 +-- Configuring done (4.1s) cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h +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/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 --- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -cp inc/stJson.h ../lib/stJson.h.tmp -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)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 --- Configuring done (2.1s) -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 --- Generating done (0.1s) --- 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 -[ 14%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' -ar: creating /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a -make[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=" -[ 17%] 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' -make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build -make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' -[ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bits.cpp -[ 20%] 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -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); - | ^~~~~~~~~~~ -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)) { - | ^ -[ 22%] 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -[ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] @@ -2887,6 +2847,16 @@ 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 14 into destination object ‘buff’ of size 8 +mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.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 +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' +cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp +mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h +[ 18%] Building CXX object CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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/sonLibString.h ../lib/sonLibString.h.tmp +mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] @@ -3027,23 +2997,84 @@ 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 14 into destination object ‘buff’ of size 8 +cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp +[ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o +-- Generating done (0.2s) +-- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h +cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp +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 +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 +make -f CMakeFiles/Makefile2 sdsl +mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h +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 +cp inc/stGraph.h ../lib/stGraph.h.tmp +mv ../lib/stGraph.h.tmp ../lib/stGraph.h +/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 8 +cp inc/stJson.h ../lib/stJson.h.tmp +make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all +mv ../lib/stJson.h.tmp ../lib/stJson.h +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 +cp inc/stMatrix.h ../lib/stMatrix.h.tmp +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=" +mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h +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 +cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp +make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' +mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h +cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp +[ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bits.cpp +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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +[ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp [ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 [ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp -[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/trivially_serializable.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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/types.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/types.cpp -[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -[ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -[ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +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)) { + | ^ In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: @@ -3121,41 +3152,45 @@ 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 14 into destination object ‘buff’ of size 8 +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_tips.cpp -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[ 18%] Linking CXX executable debug -/usr/bin/cmake -E cmake_link_script CMakeFiles/debug.dir/link.txt --verbose=1 -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -/usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/debug.dir/link.d CMakeFiles/debug.dir/debug.cpp.o -o debug -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' -[ 18%] Built target debug -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=" -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 -make[5]: Entering 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 -[ 25%] Building CXX object CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/types.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/types.cpp [ 33%] Linking CXX static library libkff.a +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +[ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 33%] Built target kff make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 50%] Building CXX object CMakeFiles/kff_example.dir/main.cpp.o +[ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +[ 25%] Linking CXX executable debug +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +/usr/bin/cmake -E cmake_link_script CMakeFiles/debug.dir/link.txt --verbose=1 +/usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/debug.dir/link.d CMakeFiles/debug.dir/debug.cpp.o -o debug +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' +[ 25%] Built target debug +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' +[ 31%] 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[ 57%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_tips.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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: @@ -3168,9 +3203,18 @@ /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 &= | ^~~~~ -[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +cc1: warning: command-line option ‘-std=c++14’ is valid 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++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 57%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o 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); @@ -3193,9 +3237,20 @@ /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +[ 66%] Linking CXX executable kff_example cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz +[ 66%] Built target kff_example +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +[ 83%] Building CXX object benchmarks/CMakeFiles/reader_bench.dir/reader.cpp.o +[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp 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); @@ -3205,87 +3260,76 @@ impl/sonLibConnectivity.c:608:9: note: call to ‘free’ here 608 | free(comp); | ^~~~~~~~~~ -[ 65%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[ 68%] 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[ 66%] Linking CXX executable kff_example -[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp -[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -[ 66%] Built target kff_example -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -[ 83%] 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 +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 65%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ar rvs lib/libgssw.a obj/gssw.o +[ 68%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o ar: creating lib/libgssw.a a - obj/gssw.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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -[ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 [100%] Linking CXX executable reader_bench -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +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=" 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/DYNAMIC/build' +make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/build +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' +[ 37%] Building CXX object CMakeFiles/rle_bwt.dir/rle_bwt.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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [100%] Built target reader_bench make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +make -f CMakeFiles/cw-bwt.dir/build.make CMakeFiles/cw-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/cw-bwt.dir/DependInfo.cmake "--color=" +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' +[ 43%] Building CXX object CMakeFiles/cw-bwt.dir/cw-bwt.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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +cc1: warning: command-line option ‘-std=c++14’ is valid 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 +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 cc1: warning: command-line option ‘-std=c++14’ is valid 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++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /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 | } | ^ +/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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp -[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -/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 | } - | ^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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); - | ^~~~~~~~~~~~ In file included from /usr/include/aarch64-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, @@ -3309,77 +3353,83 @@ /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))); | ^ -[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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-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 -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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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 | } + | ^ +[ 50%] Linking CXX executable rle_lz77_v1 +/usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v1.dir/link.txt --verbose=1 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 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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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp +[ 56%] Building CXX object CMakeFiles/benchmark.dir/benchmark.cpp.o +/usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include 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-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 +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/config.cpp +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 [ 25%] 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP 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'/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' -[ 43%] Built target rle_lz77_v1 -make -f CMakeFiles/cw-bwt.dir/build.make CMakeFiles/cw-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/cw-bwt.dir/DependInfo.cmake "--color=" -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' -[ 50%] Building CXX object CMakeFiles/cw-bwt.dir/cw-bwt.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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.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 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CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp +[ 62%] Linking CXX executable rle_lz77_v2 +/usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v2.dir/link.txt --verbose=1 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +/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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/rle_lz77_v2.dir/link.d CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -o rle_lz77_v2 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' -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' -[ 56%] 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +[ 62%] Built target rle_lz77_v2 make -f CMakeFiles/wm_string.dir/build.make CMakeFiles/wm_string.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/wm_string.dir/DependInfo.cmake "--color=" 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' -[ 62%] Building CXX object CMakeFiles/wm_string.dir/wm_string.cpp.o +[ 68%] 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp [ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa.cpp +[ 75%] Linking CXX executable h0_lz77 +/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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/h0_lz77.dir/link.d CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -o h0_lz77 +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' +[ 75%] Built target h0_lz77 +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp cc1: warning: command-line option ‘-std=c++14’ is valid 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 @@ -3390,12 +3440,13 @@ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 -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' -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest -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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm +[ 81%] Linking CXX executable rle_bwt +/usr/bin/cmake -E cmake_link_script CMakeFiles/rle_bwt.dir/link.txt --verbose=1 +/usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/rle_bwt.dir/link.d CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -o rle_bwt +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' +[ 81%] Built target rle_bwt +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp 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 @@ -3406,30 +3457,25 @@ 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 -mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm -[ 68%] Linking CXX executable rle_lz77_v2 -/usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v2.dir/link.txt --verbose=1 -mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest -[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa.cpp +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/io.cpp +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 /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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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' [ 97%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend +ranlib /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a 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[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' [100%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake -/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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' -[ 68%] Built target rle_lz77_v2 -[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp /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' @@ -3452,6 +3498,8 @@ 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 +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/louds_tree.cpp 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' @@ -3468,8 +3516,6 @@ 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' -[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp [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 @@ -3533,30 +3579,51 @@ rm -f /build/reproducible-path/vg-1.59.0+ds/include/vg.pb.h /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" && export LDFLAGS="-Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && rm -rf build-vg && mkdir build-vg && cd build-vg && PKG_CONFIG_PATH=/build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig: cmake -DCMAKE_CXX_STANDARD=14 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH="/usr;/" -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make clean && VERBOSE=1 make && make install +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/memory_management.cpp -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/io.cpp -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp +[ 87%] Linking CXX executable cw-bwt +/usr/bin/cmake -E cmake_link_script CMakeFiles/cw-bwt.dir/link.txt --verbose=1 +/usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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' +[ 87%] Built target cw-bwt +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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") Building libvgio for C++ 14 -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Could NOT find Protobuf (missing: Protobuf_DIR) No installed Protobuf has registered itself with CMake. +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp -- Found Protobuf: /usr/lib/aarch64-linux-gnu/libprotobuf.so (found version "3.21.12") Found Protobuf using FindProtobuf.cmake -- Found Threads: TRUE Using real Threads library -- Checking for module 'htslib' -- Found htslib, version 1.20 +mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest +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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm +mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest -- Checking for module 'jansson' +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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm -- Found jansson, version 2.14 +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o +mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_fs.cpp +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sd_vector.cpp Using installed libhandlegraph --- Configuring done (1.3s) +-- Configuring done (2.5s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' @@ -3573,6 +3640,8 @@ make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake +[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sfstream.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/test_libvgio.dir/build.make CMakeFiles/test_libvgio.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' @@ -3604,138 +3673,100 @@ make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 5%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/vg.pb.cc.o -MF CMakeFiles/vgio.dir/vg.pb.cc.o.d -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/vg.pb.cc -[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp -[ 75%] Linking CXX executable rle_bwt -/usr/bin/cmake -E cmake_link_script CMakeFiles/rle_bwt.dir/link.txt --verbose=1 -[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/louds_tree.cpp -/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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/rle_bwt.dir/link.d CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -o rle_bwt -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' -[ 75%] Built target rle_bwt -[ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/memory_management.cpp -mv ../bin/sonLibTests.tmp ../bin/sonLibTests -make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' -cp sonLib_daemonize.py ./bin/sonLib_daemonize.py -chmod +x ./bin/sonLib_daemonize.py -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' -. ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/reproducible-path/vg-1.59.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/reproducible-path/vg-1.59.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/reproducible-path/vg-1.59.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' -cd externalTools && make all -make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' -cd threeEdgeConnected && make all -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' -gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c -ar rc 3EdgeConnected.a *.o -ranlib 3EdgeConnected.a -rm *.o -mv 3EdgeConnected.a ../..//../sonLib/lib/ -cp inc/*.h ../..//../sonLib/lib/ -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 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-I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp -[ 87%] 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 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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' -[100%] Built target benchmark -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/ [ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o -MF CMakeFiles/sdsl.dir/simple_sds.cpp.o.d -o CMakeFiles/sdsl.dir/simple_sds.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/simple_sds.cpp [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd 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--pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a +[ 93%] Linking CXX executable wm_string +/usr/bin/cmake -E cmake_link_script CMakeFiles/wm_string.dir/link.txt --verbose=1 [ 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 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-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' +[ 93%] Built target wm_string [ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp [ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp [ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/wt_helper.cpp +[100%] 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 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'/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' +cp sonLib_daemonize.py ./bin/sonLib_daemonize.py make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" -[ 14%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time 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./deps/pinchesAndCacti && make && cd /build/reproducible-path/vg-1.59.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/reproducible-path/vg-1.59.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/reproducible-path/vg-1.59.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib +[ 14%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 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/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp -[ 35%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' +cd externalTools && make all +make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' +cd threeEdgeConnected && make all +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' +gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c +[ 17%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/basic_stream.cpp +[ 20%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/registry.cpp.o -MF CMakeFiles/vgio.dir/src/registry.cpp.o.d -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/registry.cpp +[ 47%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd 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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' @@ -3749,8 +3780,6 @@ 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 -[ 58%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio_static.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/json2pb.cpp /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' @@ -3900,58 +3929,80 @@ mkdir -p lib mkdir -p obj make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' +[ 52%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/vpkg.cpp make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp -[ 61%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp 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/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/registry.cpp -[ 70%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/stream.cpp.o -MF CMakeFiles/vgio.dir/src/stream.cpp.o.d -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream.cpp -[ 73%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream_multiplexer.cpp -[ 76%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_iterator.cpp -[ 79%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/registry.cpp.o -MF CMakeFiles/vgio_static.dir/src/registry.cpp.o.d -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/registry.cpp -[ 82%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time 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-MT CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream_multiplexer.cpp -[ 91%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio_static.dir/src/vpkg.cpp.o.d -o 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/build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gcsa.o src/gcsa.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp -[ 94%] Linking CXX shared library libvgio.so -/usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/lcp.o src/lcp.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_graph.o src/path_graph.cpp -/usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wl,--dependency-file=CMakeFiles/vgio.dir/link.d -Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/lib/aarch64-linux-gnu/libprotobuf.so -lhts -ljansson /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -[ 94%] Built target vgio -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwt && make clean && make && mv lib/libgbwt.a /build/reproducible-path/vg-1.59.0+ds/lib +. ./source_me.sh && rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/reproducible-path/vg-1.59.0+ds/include:/build/reproducible-path/vg-1.59.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" make && cp lib/libbdsg.a /build/reproducible-path/vg-1.59.0+ds/lib && cp -r bdsg/include/* /build/reproducible-path/vg-1.59.0+ds/include 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 +rm -f lib/libxg.a make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' +cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' mkdir -p bin mkdir -p lib mkdir -p obj +. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp +[ 55%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_io.cpp +[ ! -e bdsg/obj ] || rm -r bdsg/obj +[ ! -e lib ] || rm -r lib +[ ! -e bin ] || rm -r bin +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o +[ 58%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/basic_stream.cpp +[ 61%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/bwtmerge.o src/bwtmerge.cpp +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o +[ 64%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp +[ 67%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/edit.cpp.o -MF CMakeFiles/vgio_static.dir/src/edit.cpp.o.d -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/edit.cpp +[ 70%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/hfile_cppstream.cpp +[ 73%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio_static.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/json2pb.cpp +[ 76%] Linking CXX shared library libvgio.so +/usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 +[ 79%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_emitter.cpp +/usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong 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-ljansson /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +[ 79%] Built target vgio +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat 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object CMakeFiles/vgio_static.dir/src/stream.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream.cpp +[ 91%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include 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-I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/reference_path_overlay.cpp -o bdsg/obj/reference_path_overlay.o +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong 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-mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gcsa.o src/gcsa.cpp +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_reference_path_overlay.cpp -o bdsg/obj/packed_reference_path_overlay.o +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwt.o src/cached_gbwt.cpp [ 97%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 @@ -3970,6 +4021,8 @@ make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/path_subgraph_overlay.cpp -o bdsg/obj/path_subgraph_overlay.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/subgraph_overlay.cpp -o bdsg/obj/subgraph_overlay.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' @@ -4034,36 +4087,19 @@ -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -. ./source_me.sh && rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/reproducible-path/vg-1.59.0+ds/include:/build/reproducible-path/vg-1.59.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" make && cp lib/libbdsg.a /build/reproducible-path/vg-1.59.0+ds/lib && cp -r bdsg/include/* /build/reproducible-path/vg-1.59.0+ds/include -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' -[ ! -e bdsg/obj ] || rm -r bdsg/obj -[ ! -e lib ] || rm -r lib -[ ! -e bin ] || rm -r bin -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwt.o src/cached_gbwt.cpp +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dynamic_gbwt.o src/dynamic_gbwt.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/mapped_structs.cpp -o bdsg/obj/mapped_structs.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/reference_path_overlay.cpp -o bdsg/obj/reference_path_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/fast_locate.o src/fast_locate.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_reference_path_overlay.cpp -o bdsg/obj/packed_reference_path_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwt.o src/gbwt.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/path_subgraph_overlay.cpp -o bdsg/obj/path_subgraph_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/subgraph_overlay.cpp -o bdsg/obj/subgraph_overlay.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata.o src/metadata.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/lcp.o src/lcp.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/test.o src/test.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp @@ -4072,17 +4108,15 @@ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_ri.o src/build_ri.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/merge_gbwt.o src/merge_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/benchmark.o src/benchmark.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_graph.o src/path_graph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata_tool.o src/metadata_tool.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp -rm -f lib/libxg.a -cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include -. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp -ar rcs lib/libgcsa2.a obj/algorithms.o obj/dbg.o obj/files.o obj/gcsa.o obj/internal.o obj/lcp.o obj/path_graph.o obj/support.o obj/utils.o -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/mapped_structs.o bdsg/obj/packed_graph.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/reference_path_overlay.o bdsg/obj/packed_reference_path_overlay.o bdsg/obj/path_subgraph_overlay.o bdsg/obj/subgraph_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/snarl_distance_index.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp ar rcs lib/libgbwt.a obj/algorithms.o obj/bwtmerge.o obj/cached_gbwt.o obj/dynamic_gbwt.o obj/fast_locate.o obj/files.o obj/gbwt.o obj/internal.o obj/metadata.o obj/support.o obj/test.o obj/utils.o obj/variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_gbwt obj/build_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_ri obj/build_ri.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 @@ -4117,14 +4151,16 @@ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa2gbwt.o src/gfa2gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz_stats.o src/gbz_stats.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/kmer_freq.o src/kmer_freq.cpp +ar rs lib/libxg.a deps/xg/xg.o +ar: creating lib/libxg.a +ar rcs lib/libgcsa2.a obj/algorithms.o obj/dbg.o obj/files.o obj/gcsa.o obj/internal.o obj/lcp.o obj/path_graph.o obj/support.o obj/utils.o +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' ar rcs lib/libgbwtgraph.a obj/algorithms.o obj/cached_gbwtgraph.o obj/gbwtgraph.o obj/gbz.o obj/gfa.o obj/internal.o obj/minimizer.o obj/path_cover.o obj/utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/gfa2gbwt obj/gfa2gbwt.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/gbz_stats obj/gbz_stats.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/kmer_freq obj/kmer_freq.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 rm obj/kmer_freq.o obj/gbz_stats.o obj/gfa2gbwt.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' -ar rs lib/libxg.a deps/xg/xg.o -ar: creating lib/libxg.a . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp @@ -4427,7 +4463,6 @@ . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/haplotypes_main.o src/subcommand/haplotypes_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp -. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:147:31: required from here @@ -4443,6 +4478,7 @@ /usr/include/google/protobuf/message_lite.h:381:7: note: declared here 381 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ +. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp @@ -7952,63 +7988,63 @@ export PATH=$PATH:/build/reproducible-path/vg-1.59.0+ds/debian/help \ && . /build/reproducible-path/vg-1.59.0+ds/source_me.sh \ && ( cd /build/reproducible-path/vg-1.59.0+ds/test && LD_PRELOAD= prove -v t/ ) -index file /tmp/vg-xKjzYx/vg-UZClE0.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-Boh14O.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-7paqk9.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-5qZnZQ.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-tWg17k.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-Do5JJX.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-8Ykc2b.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-1NIAFZ.fai not found, generating... warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;CIPOS=0,3;CIEND=-3,0 GT ! -index file /tmp/vg-xKjzYx/vg-AqFWnC.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-ST8Oum.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-MfocRM.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-RGDusO.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-X0zuAx.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-l2pYHx.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-FsGwn5.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-p2cSP7.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-bNQ34h.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-wZNAG3.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-06y4VB.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-xuSNpq.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-zLZzl8.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-7LCSOi.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-YyOLwA.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-7Cz92q.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-CQBFOf.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-y93sSB.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-nkbXFu.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-xRJQTl.fai not found, generating... Warning: deletion END and SVLEN do not agree [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;SVLEN=-19;CIPOS=0,3;CIEND=-3,0;SPAN=19 GT END: 29 SVLEN: -19 warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;SVLEN=-19;CIPOS=0,3;CIEND=-3,0;SPAN=19 GT -index file /tmp/vg-xKjzYx/vg-UG9kyX.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-ddejNT.fai not found, generating... Warning: deletion END and SVLEN do not agree [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;SVLEN=-19;CIPOS=0,3;CIEND=-3,0;SPAN=19 GT END: 29 SVLEN: -19 warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;SVLEN=-19;CIPOS=0,3;CIEND=-3,0;SPAN=19 GT -index file /tmp/vg-xKjzYx/vg-IoJebO.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-BDp1GI.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-1kANmd.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-wa9Ulc.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-dL1QY4.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-qga1gs.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-0bvAkd.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-NLxD8T.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-m8LAsn.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-naw06F.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-ESr0EX.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-BaYI88.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-mxfzs2.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-Xepwv8.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-yDWjwQ.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-mLWcBd.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-AjT82N.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-vcsRiK.fai not found, generating... Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=18;CIPOS=0,3;SPAN=4 GT END: 18 POS: 9 warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=18;CIPOS=0,3;SPAN=4 GT -index file /tmp/vg-xKjzYx/vg-ryMRnQ.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-1QmOH1.fai not found, generating... Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=18;CIPOS=0,3;SPAN=4 GT END: 18 POS: 9 warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=18;CIPOS=0,3;SPAN=4 GT -index file /tmp/vg-xKjzYx/vg-7kwLcT.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-q4ZdEx.fai not found, generating... Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=13;CIPOS=0,3;SPAN=4 GT END: 13 POS: 9 Warning: VCF writer incorrecty produced END = POS + SVLEN for an insertion. Fixing END to POS. -index file /tmp/vg-xKjzYx/vg-0QwmEa.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-H7brgS.fai not found, generating... Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=13;CIPOS=0,3;SPAN=4 GT END: 13 POS: 9 Warning: VCF writer incorrecty produced END = POS + SVLEN for an insertion. Fixing END to POS. -index file /tmp/vg-xKjzYx/vg-r5S0oE.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-gwQnex.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-cAgbMQ.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-URAvfL.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-L15Ucv.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-hylhzq.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-41Rydo.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-NfGCnu.fai not found, generating... warning:[vg::Constructor] Lowercase characters found in x; coercing to uppercase. -index file /tmp/vg-xKjzYx/vg-wNTRy5.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-ggKlDg.fai not found, generating... warning:[vg::Constructor] Lowercase characters found in x; coercing to uppercase. -index file /tmp/vg-xKjzYx/vg-wyXIvJ.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-DvCt1D.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-ACrWkh.fai not found, generating... -index file /tmp/vg-xKjzYx/vg-ambr0h.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-tN6YDx.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-taax1z.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-iEmuKI.fai not found, generating... +index file /tmp/vg-ovYD7T/vg-qpIddJ.fai not found, generating... 2 0 3 0 iterated on 4 0 @@ -8350,7 +8386,6 @@ ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ @@ -8358,6 +8393,7 @@ ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ +warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. index file t.fa.fai not found, generating... [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. t/07_vg_map.t ......... @@ -9492,12 +9528,12 @@ [vg mpmap] elapsed time 0 s: Loading GCSA2 from g.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Loading LCP from g.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component -[vg mpmap] elapsed time 0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. +[vg mpmap] elapsed time 1 s: Completed memoizing GCSA2 queries +[vg mpmap] elapsed time 1 s: Loading LCP from g.gcsa.lcp +[vg mpmap] elapsed time 1 s: Completed loading LCP +[vg mpmap] elapsed time 1 s: Labeling embedded paths by their connected component +[vg mpmap] elapsed time 1 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread +[vg mpmap] elapsed time 1 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x g.xg -g g.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -I 10 -D 1 -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from g.xg [vg mpmap] elapsed time 0 s: Completed loading graph @@ -9684,31 +9720,31 @@ ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ +Warning: realigned read CTGTAGGGCTCA doesn't touch either end of its snarl! +Warning: realigned read CTCATTGTAACG doesn't touch either end of its snarl! Warning: realigned read TGAGCCCTACAG doesn't touch either end of its snarl! -Warning: realigned read GTAGGGCTCATT doesn't touch either end of its snarl! +Warning: realigned read TTACAATGAGCC doesn't touch either end of its snarl! +Warning: realigned read TAGGGCTCATTG doesn't touch either end of its snarl! Warning: realigned read GAGCCCTACAGA doesn't touch either end of its snarl! -Warning: realigned read GCTCATTGTAAC doesn't touch either end of its snarl! -Warning: realigned read CTGTAGGGCTCA doesn't touch either end of its snarl! -Warning: realigned read TACAATGAGCCC doesn't touch either end of its snarl! +Warning: realigned read GTAGGGCTCATT doesn't touch either end of its snarl! Warning: realigned read TGTCTGTAGGGC doesn't touch either end of its snarl! Warning: realigned read TACAATGAGCCC doesn't touch either end of its snarl! -Warning: realigned read AGGGCTCATTGT doesn't touch either end of its snarl! +Warning: realigned read CCTACAGACATA doesn't touch either end of its snarl! +Warning: realigned read TGTCTGTAGGGC doesn't touch either end of its snarl! Warning: realigned read GCTCATTGTAAC doesn't touch either end of its snarl! -Warning: realigned read GTCTGTAGGGCT doesn't touch either end of its snarl! Warning: realigned read CTGTAGGGCTCA doesn't touch either end of its snarl! +Warning: realigned read CCCTACAGACAT doesn't touch either end of its snarl! +Warning: realigned read GTCTGTAGGGCT doesn't touch either end of its snarl! +Warning: realigned read AGGGCTCATTGT doesn't touch either end of its snarl! +Warning: realigned read ACGTTACAATGA doesn't touch either end of its snarl! +Warning: realigned read GGGCTCATTGTA doesn't touch either end of its snarl! +Warning: realigned read TACAATGAGCCC doesn't touch either end of its snarl! Warning: realigned read TATGTCTGTAGG doesn't touch either end of its snarl! -Warning: realigned read TTACAATGAGCC doesn't touch either end of its snarl! +Warning: realigned read GCTCATTGTAAC doesn't touch either end of its snarl! Warning: realigned read TACAGACATATC doesn't touch either end of its snarl! Warning: realigned read GTTACAATGAGC doesn't touch either end of its snarl! -Warning: realigned read ACGTTACAATGA doesn't touch either end of its snarl! -Warning: realigned read GGGCTCATTGTA doesn't touch either end of its snarl! -Warning: realigned read CTCATTGTAACG doesn't touch either end of its snarl! -Warning: realigned read CCCTACAGACAT doesn't touch either end of its snarl! -Warning: realigned read TAGGGCTCATTG doesn't touch either end of its snarl! Warning: realigned read GCCCTACAGACA doesn't touch either end of its snarl! -Warning: realigned read TGTCTGTAGGGC doesn't touch either end of its snarl! Warning: realigned read ACGTTACAATGA doesn't touch either end of its snarl! -Warning: realigned read CCTACAGACATA doesn't touch either end of its snarl! Statistics: Number of Non-Degenerate Snarls: 1 Snarls traversed by reads: 1 @@ -9956,10 +9992,10 @@ Variant 73: 2 haplotypes at x:945: 204 bp vs. 223 bp haplotypes vs. graphs average Variant 74: 2 haplotypes at x:972: 177 bp vs. 194 bp haplotypes vs. graphs average Variant 75: 2 haplotypes at x:1000: 136 bp vs. 149 bp haplotypes vs. graphs average - -WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. +WARNING:[vg] Subcommand ' +add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. + terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ @@ -9970,10 +10006,10 @@ error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. +[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ @@ -9985,9 +10021,9 @@ error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph -WARNING:[vg] Subcommand '[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead.add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - +WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. +[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ @@ -10252,13 +10288,13 @@ [vg mpmap] elapsed time 0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries -[vg mpmap] elapsed time 1 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 1 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp -[vg mpmap] elapsed time 1 s: Completed loading LCP -[vg mpmap] elapsed time 1 s: Labeling embedded paths by their connected component -[vg mpmap] elapsed time 1 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread +[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries +[vg mpmap] elapsed time 0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp +[vg mpmap] elapsed time 0 s: Completed loading LCP +[vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component +[vg mpmap] elapsed time 0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread warning:[vg mpmap] Could not find 1000 (-b) unambiguous read pair mappings to estimate fragment length ditribution. This can happen due to data issues (e.g. unpaired reads being mapped as pairs) or because the sample size is too large for the read set. Mapping read pairs as independent single-ended reads. -[vg mpmap] elapsed time 1 s: Mapping finished. Mapped 1 read pairs. +[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -G input.gam -I 500 -D 100 -n dna -i -F GAM --no-qual-adjust [vg mpmap] elapsed time 0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0 s: Completed loading graph @@ -10295,8 +10331,8 @@ [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading distance index -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed loading LCP +[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Mapping reads from s.fq using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. @@ -10309,8 +10345,8 @@ [vg mpmap] elapsed time 0 s: Loading distance index from s.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from s.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Completed loading LCP +[vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Mapping reads from s.fq using 12 threads @@ -10324,8 +10360,8 @@ [vg mpmap] elapsed time 0 s: Loading distance index from s.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from s.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Completed loading distance index +[vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Mapping reads from s.fq using 12 threads @@ -10355,16 +10391,16 @@ [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy.gcsa [vg mpmap] elapsed time 0 s: Loading distance index from xy.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Loading LCP from xy.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading distance index +[vg mpmap] elapsed time 0 s: Loading LCP from xy.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: No reference path file given. Interpreting all non-alt-allele paths in graph as reference sequences. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg mpmap] elapsed time 0 s: Building null model to calibrate mismapping detection -[vg mpmap] elapsed time 9 s: Mapping reads from x.gam using 12 threads -[vg mpmap] elapsed time 9 s: Mapping finished. Mapped 1000 read pairs. +[vg mpmap] elapsed time 11 s: Mapping reads from x.gam using 12 threads +[vg mpmap] elapsed time 11 s: Mapping finished. Mapped 1000 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x xy.xg -d xy.dist -g xy.gcsa -G x.gam -F SAM -M 1 [vg mpmap] elapsed time 0 s: Loading graph from xy.xg [vg mpmap] elapsed time 0 s: Completed loading graph @@ -10374,15 +10410,15 @@ [vg mpmap] elapsed time 0 s: Loading distance index from xy.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from xy.gcsa.lcp -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed loading distance index +[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: No reference path file given. Interpreting all non-alt-allele paths in graph as reference sequences. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg mpmap] elapsed time 0 s: Building null model to calibrate mismapping detection -[vg mpmap] elapsed time 11 s: Mapping reads from x.gam using 12 threads -[vg mpmap] elapsed time 11 s: Mapping finished. Mapped 2000 reads. +[vg mpmap] elapsed time 15 s: Mapping reads from x.gam using 12 threads +[vg mpmap] elapsed time 15 s: Mapping finished. Mapped 2000 reads. t/33_vg_mpmap.t ....... 1..21 ok 1 - MAPQ is 50% without haplotype info @@ -10817,7 +10853,7 @@ [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. warning:[GFAParser] Skipping GFA P line: GFA format error: On pass 1: On line 27: Duplicate path GRCh38.chr1 exists in graph index file ref.fa.fai not found, generating... -warning: Thread 4 encountered sequence of length 275, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. +warning: Thread 2 encountered sequence of length 275, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. alignment: valid graph: valid warning: Thread 0 encountered sequence of length 275, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. @@ -11345,7 +11381,7 @@ [vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread -[vg mpmap] elapsed time 1 s: Mapping finished. Mapped 20 reads. +[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -w rpvg -r small/x.fa -r small/y.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/xy.gtf [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. @@ -11631,7 +11667,7 @@ Failed test: 23 t/50_vg_giraffe.t (Wstat: 0 Tests: 50 Failed: 13) Failed tests: 20-29, 48-50 -Files=53, Tests=1138, 493 wallclock secs ( 0.52 usr 0.21 sys + 718.89 cusr 221.05 csys = 940.67 CPU) +Files=53, Tests=1138, 559 wallclock secs ( 0.59 usr 0.20 sys + 736.86 cusr 254.97 csys = 992.62 CPU) Result: FAIL make[1]: [debian/rules:93: override_dh_auto_test-arch] Error 1 (ignored) make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' @@ -11672,9 +11708,9 @@ make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_md5sums dh_builddeb +dpkg-deb: building package 'vg' in '../vg_1.59.0+ds-0.1_arm64.deb'. dpkg-deb: building package 'vg-dbgsym' in '../vg-dbgsym_1.59.0+ds-0.1_arm64.deb'. dpkg-deb: building package 'vg-docs' in '../vg-docs_1.59.0+ds-0.1_all.deb'. -dpkg-deb: building package 'vg' in '../vg_1.59.0+ds-0.1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../vg_1.59.0+ds-0.1_arm64.buildinfo dpkg-genchanges --build=binary -O../vg_1.59.0+ds-0.1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -11682,12 +11718,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3891550/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3891550/tmp/hooks/B01_cleanup finished 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/2636781 and its subdirectories -I: Current time: Sat Jan 17 23:37:28 -12 2026 -I: pbuilder-time-stamp: 1768736248 +I: removing directory /srv/workspace/pbuilder/3891550 and its subdirectories +I: Current time: Mon Dec 16 19:39:47 +14 2024 +I: pbuilder-time-stamp: 1734327587