Diff of the two buildlogs: -- --- b1/build.log 2024-11-24 16:08:43.668727721 +0000 +++ b2/build.log 2024-11-24 17:44:38.384432686 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Dec 27 09:28:42 -12 2025 -I: pbuilder-time-stamp: 1766870922 +I: Current time: Mon Nov 25 06:09:04 +14 2024 +I: pbuilder-time-stamp: 1732464544 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/2027625/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2598675/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +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 Nov 24 16:09 /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/2598675/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2598675/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + 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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='b2f48b63428f4ce5a46bd0722a51613e' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2027625' - PS1='# ' - PS2='> ' + INVOCATION_ID=ad3bd28e6e584a64b48dc64baa32c8b4 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-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=2598675 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.4o9ZkNWR/pbuilderrc_xl91 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.4o9ZkNWR/b1 --logfile b1/build.log vg_1.59.0+ds-0.1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.4o9ZkNWR/pbuilderrc_NLYR --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.4o9ZkNWR/b2 --logfile b2/build.log vg_1.59.0+ds-0.1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2027625/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2598675/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 amd64 samtools amd64 1.20-3 [653 kB] Get: 381 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.20+ds-2 [486 kB] Get: 382 http://deb.debian.org/debian unstable/main amd64 xxd amd64 2:9.1.0861-1 [98.1 kB] -Fetched 265 MB in 19s (13.7 MB/s) +Fetched 265 MB in 8s (31.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package m4. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19966 files and directories currently installed.) @@ -1871,8 +1903,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Dec 27 21:31:04 UTC 2025. -Universal Time is now: Sat Dec 27 21:31:04 UTC 2025. +Local time is now: Sun Nov 24 16:12:13 UTC 2024. +Universal Time is now: Sun Nov 24 16:12:13 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libsysprof-capture-4-dev:amd64 (47.1-1) ... @@ -2222,7 +2254,11 @@ 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/2598675/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2598675/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 @@ -2235,7 +2271,7 @@ make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' find /build/reproducible-path/vg-1.59.0+ds/include/ -type f -a '!' -name vg_git_version.hpp -delete dh_auto_clean || true - make -j42 clean + make -j20 clean make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC @@ -2260,16 +2296,16 @@ cd externalTools && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' +rm -rf ../bin ../lib +make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' cd cutest && make clean cd quicktree_1.1 && make clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' -rm -rf ../bin ../lib -make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' -rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' +rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' @@ -2280,7 +2316,7 @@ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' make[2]: *** [Makefile:854: clean] Error 2 make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' -dh_auto_clean: error: make -j42 clean returned exit code 2 +dh_auto_clean: error: make -j20 clean returned exit code 2 make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' @@ -2350,7 +2386,7 @@ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' make[2]: *** [Makefile:854: clean] Error 2 make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' - make -j42 "INSTALL=install --strip-program=true" SFX=-avx2 all test/build_graph bin/shuf + make -j20 "INSTALL=install --strip-program=true" SFX=-avx2 all test/build_graph bin/shuf make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC @@ -2366,59 +2402,48 @@ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp -r src/include/structures /build/reproducible-path/vg-1.59.0+ds/include/ rm -f lib/cleaned_old_protobuf* cp deps/BBHash/BooPHF.h /build/reproducible-path/vg-1.59.0+ds/include -rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' -gcc -c -o ssw.o ssw.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. cp -r deps/sparsepp/sparsepp include/ -g++ -c -o ssw_cpp.o ssw_cpp.cpp -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. +rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc rm -Rf include/dynamic.hpp include/dynamic -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' -gcc -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c -rm -Rf include/google/protobuf deps/protobuf +. ./source_me.sh && cp -r deps/mio/include/mio /build/reproducible-path/vg-1.59.0+ds/include/ +. ./source_me.sh && cp -r deps/atomic_queue/include/atomic_queue/* /build/reproducible-path/vg-1.59.0+ds/include/ Library will be installed in '/build/reproducible-path/vg-1.59.0+ds' -gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c +. ./source_me.sh && cp -r deps/ips4o/ips4o* /build/reproducible-path/vg-1.59.0+ds/include/ # annoyingly doesn't have an install option on the cmake, so we manually move their external dependency headers -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' +rm -Rf include/google/protobuf deps/protobuf make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd externalTools && make all -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -touch lib/cleaned_old_protobuf_v003 +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' +gcc -c -o ssw.o ssw.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC && rm -Rf build && mkdir -p build && cd build && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" && cmake -DCMAKE_VERBOSE_MAKEFILE=ON .. && make -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' -if [ ! -d bin ]; then mkdir -p bin; fi +gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c +g++ -c -o ssw_cpp.o ssw_cpp.cpp -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. +touch lib/cleaned_old_protobuf_v003 +gcc -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c +cd ./deps/lru_cache && cp *.h* /build/reproducible-path/vg-1.59.0+ds/include/ +WARNING: .git/hooks directory does not exists. + 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 +cp deps/sha1/*.h* /build/reproducible-path/vg-1.59.0+ds/include/ +cp deps/progress_bar/progress_bar.hpp /build/reproducible-path/vg-1.59.0+ds/include +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/ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cd quicktree_1.1 && make all CC="gcc -std=c99" -WARNING: .git/hooks directory does not exists. - The pre-commit hook is not installed. -. ./source_me.sh && cp -r deps/mio/include/mio /build/reproducible-path/vg-1.59.0+ds/include/ -. ./source_me.sh && cp -r deps/atomic_queue/include/atomic_queue/* /build/reproducible-path/vg-1.59.0+ds/include/ -rm -f /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/* make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' -. ./source_me.sh && cp -r deps/ips4o/ips4o* /build/reproducible-path/vg-1.59.0+ds/include/ +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' +if [ ! -d bin ]; then mkdir -p bin; fi gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c -if [ ! -d obj ]; then mkdir -p obj; fi -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' -cd ./deps/lru_cache && cp *.h* /build/reproducible-path/vg-1.59.0+ds/include/ make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c -cp deps/sha1/*.h* /build/reproducible-path/vg-1.59.0+ds/include/ -cp deps/progress_bar/progress_bar.hpp /build/reproducible-path/vg-1.59.0+ds/include -gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' -if [ ! -d lib ]; then mkdir -p lib; fi +gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c +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/* gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c -mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/dozeu && cp deps/dozeu/*.h /build/reproducible-path/vg-1.59.0+ds/include/dozeu/ gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj; fi -gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o -find bin obj lib -type f -delete -gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. @@ -2429,9 +2454,7 @@ -- Setting build type to 'Release' as none was specified. -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test; fi -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o +if [ ! -d obj ]; then mkdir -p 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. @@ -2441,32 +2464,11 @@ to work with policies introduced by or earlier. -if [ ! -d bin ]; then mkdir -p bin; fi -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o -if [ ! -d obj ]; then mkdir -p obj; fi -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin; fi -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o +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 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c if [ ! -d lib ]; then mkdir -p lib; fi -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib; fi -. ./source_me.sh && g++ -I -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/progress_bar.o deps/progress_bar/progress_bar.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/union_find.cpp -o obj/union_find.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o -g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps; fi -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o -ln -s `which shuf` bin/shuf -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o -diff: include/vg_environment_version.hpp: No such file or directory -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o -. ./source_me.sh && cp deps/mmmultimap/src/mmmultimap.hpp deps/mmmultimap/src/mmmultiset.hpp /build/reproducible-path/vg-1.59.0+ds/include/ +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 ./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 ); @@ -2474,6 +2476,27 @@ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +find bin obj lib -type f -delete +if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test; fi +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' +gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' +if [ ! -d bin ]; then mkdir -p bin; fi +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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/union_find.cpp -o obj/union_find.o +diff: include/vg_environment_version.hppif [ ! -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 +: No such file or directory +gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c +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 +. ./source_me.sh && g++ -I -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/progress_bar.o deps/progress_bar/progress_bar.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o +-- The C compiler identification is GNU 14.2.0 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o +-- The C compiler identification is GNU 14.2.0 ./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); @@ -2481,7 +2504,6 @@ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ --- The C compiler identification is GNU 14.2.0 ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2504,85 +2526,28 @@ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ --- The C compiler identification is GNU 14.2.0 --- The C compiler identification is GNU 14.2.0 --- The CXX compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 --- Detecting C compiler ABI info -/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: -/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] - 20 | } - | ^ +-- The C compiler identification is GNU 14.2.0 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- The C compiler identification is GNU 14.2.0 --- Detecting CXX compiler ABI info -- The CXX compiler identification is GNU 14.2.0 ar rc cuTest.a *.o --- Detecting C compiler ABI info +-- Detecting CXX compiler ABI info +-- The CXX compiler identification is GNU 14.2.0 ranlib cuTest.a rm -f *.o +-- Detecting C compiler ABI info mv cuTest.a ../../lib/ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o cp CuTest.h ../../lib/ -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' --- Detecting C compiler ABI info - done --- Detecting C compiler ABI info - done --- Detecting CXX compiler ABI info - done --- Check for working C compiler: /usr/bin/gcc - skipped --- Detecting C compile features --- Detecting C compile features - done --- Check for working C compiler: /usr/bin/gcc - skipped --- Detecting C compile features --- Detecting C compile features - done --- Detecting C compiler ABI info - done --- Check for working CXX compiler: /usr/bin/g++ - skipped --- Detecting CXX compile features --- Detecting CXX compile features - done --- Detecting CXX compiler ABI info --- Detecting CXX compiler ABI info -- Detecting C compiler ABI info --- Check for working C compiler: /usr/bin/cc - skipped --- Detecting C compile features --- Detecting C compile features - done --- Detecting CXX compiler ABI info -/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: -/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] - 96 | } - | ^ --- Detecting CXX compiler ABI info - done --- Detecting CXX compiler ABI info - done --- Detecting C compiler ABI info - done --- Check for working CXX compiler: /usr/bin/g++ - skipped --- Detecting CXX compile features --- Detecting CXX compile features - done --- Detecting CXX compiler ABI info - done -libhandlegraph is root project or external_project-- Check for working C compiler: /usr/bin/gcc - skipped - --- Detecting C compile features --- Detecting C compile features - done --- Check for working CXX compiler: /usr/bin/g++ - skipped --- Configuring done (1.9s) --- Detecting CXX compile features --- Detecting CXX compile features - done --- Compiler is recent enough to support C++14. --- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG --- Configuring done (1.9s) --- Generating done (0.0s) --- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --- Generating done (0.0s) -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -/usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 --- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build --- Check for working CXX compiler: /usr/bin/c++ - skipped --- Detecting CXX compile features --- Detecting CXX compile features - done -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks -Building in Release mode --- Configuring done (2.0s) -make -f CMakeFiles/Makefile2 all -make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o src/gssw.c: In function ‘gssw_graph_print’: src/gssw.c:1947:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1947 | fprintf(stdout, "GRAPH // node %llu %u %s\n", n->id, n->len, n->seq); @@ -2591,8 +2556,6 @@ | | uint64_t {aka long unsigned int} | long long unsigned int | %lu -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" src/gssw.c:1951:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1951 | fprintf(stdout, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~~~~~~~~~~ @@ -2633,10 +2596,6 @@ | | uint64_t {aka long unsigned int} | long long unsigned int | %lu -make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' --- Generating done (0.1s) --- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' src/gssw.c: In function ‘gssw_print_graph_cigar’: src/gssw.c:3623:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 3623 | fprintf(out, "%llu[", nc->node->id); @@ -2645,13 +2604,7 @@ | | uint64_t {aka long unsigned int} | long long unsigned int | %lu -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -/usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC -B/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build --check-build-system CMakeFiles/Makefile.cmake 0 src/gssw.c: In function ‘gssw_create_seed_byte’: -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' src/gssw.c:5095:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5095 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); | ~~~^ ~~~~~~~~~~~ @@ -2659,7 +2612,6 @@ | | uint64_t {aka long unsigned int} | long long unsigned int | %lu -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' src/gssw.c: In function ‘gssw_create_seed_word’: src/gssw.c:5130:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5130 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); @@ -2668,205 +2620,172 @@ | | uint64_t {aka long unsigned int} | long long unsigned int | %lu -[ 2%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp -[ 5%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o -[ 8%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dfs.cpp -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/handle_graph.cpp -[ 11%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_metadata.cpp -[ 14%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build//CMakeFiles/progress.marks -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/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 -[ 16%] Building CXX object CMakeFiles/kff.dir/kff_io.cpp.o -[ 17%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o -[ 20%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -[ 22%] 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_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 -[ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp -[ 28%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp -[ 34%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -[ 34%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_handle_graph.cpp -[ 37%] 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=. 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-I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/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 -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 -[ 40%] 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 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-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 -[ 60%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp -[ 62%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/count_walks.cpp --- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success -rm -f lib/libstructures.a -ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o -ar: creating lib/libstructures.a -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' -[ 65%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -MF 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 -[ 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp -[ 71%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp --- Performing Test HAVE_CXA_DEMANGLE -[ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP 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/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 +-- Detecting C compiler ABI info - done +/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 | } + | ^ +-- Check for working C compiler: /usr/bin/gcc - skipped +-- Detecting C compile features +-- Detecting C compile features - done +-- Detecting C compiler ABI info - done +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o +-- 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 CXX compiler ABI info - done +-- Check for working C compiler: /usr/bin/cc - skipped +-- Detecting C compile features +-- Detecting C compile features - done +-- Detecting CXX compiler ABI info +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o +-- Detecting CXX compiler ABI info +-- Check for working CXX compiler: /usr/bin/g++ - skipped +-- Detecting CXX compile features +-- Detecting CXX compile features - done +-- Detecting C compiler ABI info +/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: +/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] + 96 | } + | ^ +-- Detecting CXX compiler ABI info - done gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm -[ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g 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have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build +-- Detecting C compiler ABI info - done cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp -cp inc/hashTableC.h ../lib/hashTableC.h.tmp +-- Check for working CXX compiler: /usr/bin/c++ - skipped +-- Detecting CXX compile features +-- Detecting CXX compile features - done mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h +-- Configuring done (2.6s) +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +/usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 +-- Generating done (0.0s) +cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h +-- Check for working C compiler: /usr/bin/gcc - skipped +-- Detecting C compile features +-- Detecting C compile features - done +-- Build files have been written to: /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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o +/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 cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +-- Compiler is recent enough to support C++14. +-- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h +Building in Release mode cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h -[ 82%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o +-- Configuring done (2.8s) +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/reverse_complement.cpp +make -f CMakeFiles/Makefile2 all +-- Generating done (0.0s) +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 mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h +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' +-- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h +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 cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp +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' mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp +ln -s `which shuf` bin/shuf +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 +[ 16%] Building CXX object CMakeFiles/kff.dir/kff_io.cpp.o +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp -cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp +. ./source_me.sh && cp deps/mmmultimap/src/mmmultimap.hpp deps/mmmultimap/src/mmmultiset.hpp /build/reproducible-path/vg-1.59.0+ds/include/ +/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 mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h +cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h +make -f CMakeFiles/Makefile2 all +make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' +make -f CMakeFiles/debug.dir/build.make CMakeFiles/debug.dir/depend +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' +cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles/debug.dir/DependInfo.cmake "--color=" +[ 2%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h +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 -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/depend +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp +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=" +[ 6%] Building CXX object CMakeFiles/debug.dir/debug.cpp.o mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h +/usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/debug.dir/debug.cpp.o -MF CMakeFiles/debug.dir/debug.cpp.o.d -o CMakeFiles/debug.dir/debug.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/debug.cpp cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp -[ 85%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/split_strands.cpp +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 cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h +[ 12%] Building CXX object CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o +/usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -MF CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o.d -o CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/rle_lz77_v1.cpp cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h -[ 88%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/chop.cpp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp +-- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG - Success +-- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h @@ -2874,66 +2793,117 @@ mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.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/sonLibTuples.h ../lib/sonLibTuples.h.tmp +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 mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h +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=" cp inc/stGraph.h ../lib/stGraph.h.tmp +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' mv ../lib/stGraph.h.tmp ../lib/stGraph.h +[ 25%] Building CXX object CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o +[ 25%] Building CXX object CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o cp inc/stJson.h ../lib/stJson.h.tmp +/usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -MF CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o.d -o CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/h0_lz77.cpp mv ../lib/stJson.h.tmp ../lib/stJson.h +/usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -MF CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o.d -o CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/rle_lz77_v2.cpp cp inc/stMatrix.h ../lib/stMatrix.h.tmp -[ 91%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp +rm -f lib/libstructures.a +ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h +ar: creating lib/libstructures.a cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp +src/gssw.c: In function ‘gssw_sw_software_byte’: +src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] + 277 | memcpy(scratch, to_unswizzle, size); + | ^ +In function ‘unswizzle_byte’, + inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: +src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ + 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -o ssw_test ssw.o main.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. -lm -lz +make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/depend +gcc -o example_c ssw.o example.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. -lm -lz mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' +cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_bwt.dir/DependInfo.cmake "--color=" cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp --- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h --- Could NOT find Git (missing: GIT_EXECUTABLE) -CMake Warning at CMakeLists.txt:102 (message): - git not found. Cloning of submodules will not work. - - cp inc/stSafeC.h ../lib/stSafeC.h.tmp --- Looking for C++ include cstdio mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h +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 cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h +[ 31%] 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -MF CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o.d -o CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/rle_bwt.cpp cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp -mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h -gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -I inc -I ../lib/ -c impl/*.c -[ 94%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/extend.cpp -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C --- Looking for C++ include cstdio - found --- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot --- Configuring done (8.7s) -gcc -o ssw_test ssw.o main.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. -lm -lz -gcc -o example_c ssw.o example.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. -lm -lz +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' g++ -o example_cpp example.cpp ssw.o ssw_cpp.o -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -pipe -O3 -I. -lm -lz +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=" cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ --- Generating done (0.6s) --- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' -/usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 +mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h +[ 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dfs.cpp +gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -I inc -I ../lib/ -c impl/*.c +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' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -make -f CMakeFiles/Makefile2 sdsl -make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' -/usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 -/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 8 -src/gssw.c: In function ‘gssw_sw_software_byte’: -src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] - 277 | memcpy(scratch, to_unswizzle, size); +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 /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles/benchmark.dir/DependInfo.cmake "--color=" +[ 37%] 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -MF CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o.d -o CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/cw-bwt.cpp +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/benchmark.dir/build.make CMakeFiles/benchmark.dir/build +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' +make -f CMakeFiles/wm_string.dir/build.make CMakeFiles/wm_string.dir/build +[ 8%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/handle_graph.cpp +[ 43%] Building CXX object CMakeFiles/benchmark.dir/benchmark.cpp.o +[ 50%] Building CXX object CMakeFiles/wm_string.dir/wm_string.cpp.o +/usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/wm_string.dir/wm_string.cpp.o -MF CMakeFiles/wm_string.dir/wm_string.cpp.o.d -o CMakeFiles/wm_string.dir/wm_string.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/wm_string.cpp +/usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/benchmark.dir/benchmark.cpp.o -MF CMakeFiles/benchmark.dir/benchmark.cpp.o.d -o CMakeFiles/benchmark.dir/benchmark.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/benchmark.cpp +[ 11%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/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 +-- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success +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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 14%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_metadata.cpp +[ 17%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 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'/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" -make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' -make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build -make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' -[ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI 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/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/io.cpp -[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/memory_management.cpp -[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/louds_tree.cpp -[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp -[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_fs.cpp -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' -ar: creating /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a -[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sd_vector.cpp -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sfstream.cpp -src/gssw.c: In function ‘gssw_sw_software_word’: -src/gssw.c:1117:5: warning: ‘__builtin_memcpy’ writing between 18446744069414584336 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] - 1117 | memcpy(scratch, to_unswizzle, size * sizeof(int16_t)); - | ^ -In function ‘unswizzle_word’, - inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: -src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ - 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o -MF CMakeFiles/sdsl.dir/simple_sds.cpp.o.d -o CMakeFiles/sdsl.dir/simple_sds.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/simple_sds.cpp -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/structure_tree.cpp -[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint128_t.cpp -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp -[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp -In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/vector:63, - from /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:8: -In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = long int]’, - inlined from ‘static void std::allocator_traits >::deallocate(allocator_type&, pointer, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:544:23, - inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:389:19, - inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:368:15, - inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:738:7, - inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:445:5: -/usr/include/c++/14/bits/new_allocator.h:172:33: warning: ‘void operator delete(void*, std::size_t)’ called on pointer ‘’ with nonzero offset [1, 9223372036854775800] [-Wfree-nonheap-object] - 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); - | ^ -In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = long int]’, - inlined from ‘static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:509:28, - inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:380:33, - inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:398:44, - inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:334:26, - inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const value_type&, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:571:47, - inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:327:85: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from ‘void* operator new(std::size_t)’ - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/wt_helper.cpp src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4975:5: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 4975 | strncpy(n->seq, seq, len); n->seq[len] = 0; @@ -3063,34 +2932,126 @@ src/gssw.c:4971:19: note: length computed here 4971 | int32_t len = strlen(seq); | ^~~~~~~~~~~ +[ 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' +ar: creating /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a +[ 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -In file included from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, - from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, - from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: -In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, - inlined from ‘static void 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CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/reproducible-path/vg-1.59.0+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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/types.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/types.cpp [ 56%] Linking CXX executable debug /usr/bin/cmake -E cmake_link_script CMakeFiles/debug.dir/link.txt --verbose=1 +[ 42%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o -[ 56%] Built target debug [ 33%] Linking CXX static library libkff.a +/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 8 +make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all +[ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dijkstra.cpp +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' +make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend +make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" +make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' +make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build +make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' +[ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o +[ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_acyclic.cpp +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bits.cpp +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 82%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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CMakeFiles/kff_example.dir/main.cpp.o +[ 85%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/split_strands.cpp +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/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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' +[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp +[ 88%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/chop.cpp +[ 91%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp +gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 94%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/extend.cpp +[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] @@ -3114,25 +3075,45 @@ /usr/include/lz4.h:774:68: note: declared here 774 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -# Make dest directory -gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz ar rvs lib/libgssw.a obj/gssw.o -gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz ar: creating lib/libgssw.a a - obj/gssw.o -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' -[ 33%] Built target kff -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +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_fibonacci.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/vector:63, + from /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:8: +In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = long int]’, + inlined from ‘static void std::allocator_traits >::deallocate(allocator_type&, pointer, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:544:23, + inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:389:19, + inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:368:15, + inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:738:7, + inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:445:5: +/usr/include/c++/14/bits/new_allocator.h:172:33: warning: ‘void operator delete(void*, std::size_t)’ called on pointer ‘’ with nonzero offset [1, 9223372036854775800] [-Wfree-nonheap-object] + 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); + | ^ +In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = long int]’, + inlined from ‘static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:509:28, + inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:380:33, + inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:398:44, + inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:334:26, + inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const value_type&, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:571:47, + inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:327:85: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from ‘void* operator new(std::size_t)’ + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -[ 50%] Building CXX object CMakeFiles/kff_example.dir/main.cpp.o [ 66%] Building CXX object benchmarks/CMakeFiles/reader_bench.dir/reader.cpp.o +[ 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/config.cpp +[ 83%] Linking CXX executable kff_example +[ 62%] Linking CXX executable wm_string +/usr/bin/cmake -E cmake_link_script CMakeFiles/wm_string.dir/link.txt --verbose=1 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); @@ -3142,61 +3123,129 @@ impl/sonLibConnectivity.c:608:9: note: call to ‘free’ here 608 | free(comp); | ^~~~~~~~~~ -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' -[ 83%] Linking CXX executable reader_bench -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[ 62%] Linking CXX executable wm_string -/usr/bin/cmake -E cmake_link_script CMakeFiles/wm_string.dir/link.txt --verbose=1 +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/wm_string.dir/link.d CMakeFiles/wm_string.dir/wm_string.cpp.o -o wm_string make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 62%] Built target wm_string +[ 83%] Built target kff_example +[ 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_config.cpp +[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_isa.cpp +[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp [ 68%] Linking CXX executable benchmark -/usr/bin/cmake -E cmake_link_script CMakeFiles/benchmark.dir/link.txt --verbose=1 -[ 83%] Built target reader_bench cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +/usr/bin/cmake -E cmake_link_script CMakeFiles/benchmark.dir/link.txt --verbose=1 +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' +[100%] Linking CXX executable reader_bench +[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp +[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.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 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/benchmark.dir/link.d CMakeFiles/benchmark.dir/benchmark.cpp.o -o benchmark make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' -[ 68%] Built target benchmark -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[100%] Linking CXX executable kff_example +[ 75%] Linking CXX executable cw-bwt +[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o +/usr/bin/cmake -E cmake_link_script CMakeFiles/cw-bwt.dir/link.txt --verbose=1 +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/io.cpp +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp +[ 75%] Built target benchmark +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -[ 75%] Linking CXX executable h0_lz77 -[100%] Built target kff_example -/usr/bin/cmake -E cmake_link_script CMakeFiles/h0_lz77.dir/link.txt --verbose=1 +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/louds_tree.cpp +/usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/cw-bwt.dir/link.d "CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o" -o cw-bwt +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/memory_management.cpp +[ 81%] Linking CXX executable rle_bwt +/usr/bin/cmake -E cmake_link_script CMakeFiles/rle_bwt.dir/link.txt --verbose=1 +In file included from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, + from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, + from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: +In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, + inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, + inlined from ‘void sdsl::int_vector< >::bit_resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1358:27, + inlined from ‘void sdsl::int_vector< >::resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:380:23, + inlined from ‘sdsl::int_vector< >::int_vector(size_type, value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1285:11, + inlined from ‘sdsl::excess::impl::impl()’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: +/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:448:9: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] + 448 | *word &= + | ^~~~~ +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 81%] Built target cw-bwt +[100%] Built target reader_bench make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -/usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/h0_lz77.dir/link.d CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -o h0_lz77 +/usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/rle_bwt.dir/link.d CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -o rle_bwt make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' -[ 75%] Built target h0_lz77 -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[ 81%] Linking CXX executable cw-bwt -/usr/bin/cmake -E cmake_link_script CMakeFiles/cw-bwt.dir/link.txt --verbose=1 -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/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 rle_lz77_v2 +[ 87%] Built target rle_bwt +/usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v2.dir/link.txt --verbose=1 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -/usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/cw-bwt.dir/link.d "CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o" -o cw-bwt +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_fs.cpp +/usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/rle_lz77_v2.dir/link.d CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -o rle_lz77_v2 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' -[ 81%] Built target cw-bwt -[ 87%] Linking CXX executable rle_lz77_v1 -/usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v1.dir/link.txt --verbose=1 -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -[ 93%] Linking CXX executable rle_bwt -/usr/bin/cmake -E cmake_link_script CMakeFiles/rle_bwt.dir/link.txt --verbose=1 +[ 87%] Built target rle_lz77_v2 +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -/usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/rle_bwt.dir/link.d CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -o rle_bwt +[ 93%] Linking CXX executable h0_lz77 +/usr/bin/cmake -E cmake_link_script CMakeFiles/h0_lz77.dir/link.txt --verbose=1 +[100%] Linking CXX executable rle_lz77_v1 +/usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v1.dir/link.txt --verbose=1 +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sd_vector.cpp +/usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/h0_lz77.dir/link.d CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -o h0_lz77 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/rle_lz77_v1.dir/link.d CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -o rle_lz77_v1 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sfstream.cpp +[100%] Built target h0_lz77 +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o -MF CMakeFiles/sdsl.dir/simple_sds.cpp.o.d -o CMakeFiles/sdsl.dir/simple_sds.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/simple_sds.cpp +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/structure_tree.cpp +[100%] Built target rle_lz77_v1 +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/ +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint128_t.cpp +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/wt_helper.cpp +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 94%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend +make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" -make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' @@ -3205,42 +3254,33 @@ make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +[ 97%] Linking CXX static library libhandlegraph.a [100%] Linking CXX shared library libhandlegraph.so -[100%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 -[ 93%] Built target rle_bwt -[ 93%] Built target rle_lz77_v1 -/usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +/usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,--dependency-file,CMakeFiles/handlegraph_shared.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Built target handlegraph_shared cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -[100%] Linking CXX executable rle_lz77_v2 -/usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v2.dir/link.txt --verbose=1 [100%] Built target handlegraph_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" -/usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/rle_lz77_v2.dir/link.d CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -o rle_lz77_v2 -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' -[100%] Built target rle_lz77_v2 -make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' -/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles 0 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' @@ -3250,24 +3290,21 @@ make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' -# Do the copy of the main file last so we can tell if this recipe failed and redo it. -# Otherwise we get dynamic.hpp without its deps -mkdir -p include/dynamic && cp -r /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include/dynamic/* include/dynamic/ [ 97%] Built target handlegraph_static make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Built target handlegraph_shared make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 @@ -3279,50 +3316,57 @@ /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so +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); + | ^~~~~~~~~~~~ -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.a -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_deletable_handle_graph.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_metadata.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_metadata.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_position_handle_graph.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_handle_graph.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/deletable_handle_graph.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_handle_graph.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/expanding_overlay_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/util.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/buildable_snarl_decomposition.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/trivially_serializable.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/iteratee.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_handle_graph.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_metadata.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/types.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/snarl_decomposition.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/named_node_back_translation.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_metadata.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_tips.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/count_walks.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/split_strands.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/eades_algorithm.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/are_equivalent.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dijkstra.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/append_graph.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/apply_orientations.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal/dfs.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dagify.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/reverse_complement.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_shortest_paths.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/topological_sort.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/copy_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/strongly_connected_components.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/chop.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/extend.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/weakly_connected_components.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_single_stranded.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/chop.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_shortest_paths.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/are_equivalent.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_acyclic.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_handle_graph.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/handle_graph.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/snarl_decomposition.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/types.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/named_node_back_translation.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dijkstra.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/append_graph.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/apply_orientations.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_single_stranded.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/count_walks.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/weakly_connected_components.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/eades_algorithm.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/topological_sort.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/copy_graph.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_tips.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dagify.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/expanding_overlay_graph.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/trivially_serializable.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/iteratee.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_handle_graph.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/deletable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable_handle_graph.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_mutable_handle_graph.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_position_handle_graph.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphConfig.cmake @@ -3332,56 +3376,53 @@ rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" && export LDFLAGS="-Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && rm -rf build-vg && mkdir build-vg && cd build-vg && PKG_CONFIG_PATH=/build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig: cmake -DCMAKE_CXX_STANDARD=14 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH="/usr;/" -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make clean && VERBOSE=1 make && make install cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -impl/sonLibTreap.c: In function ‘stTreap_remove’: -impl/sonLibTreap.c:331:18: warning: pointer ‘rmnode’ used after ‘free’ [-Wuse-after-free] - 331 | stTreap *p = rmnode->parent; - | ^ -impl/sonLibTreap.c:329:9: note: call to ‘free’ here - 329 | free(rmnode); - | ^~~~~~~~~~~~ -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") Building libvgio for C++ 14 -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Could NOT find Protobuf (missing: Protobuf_DIR) No installed Protobuf has registered itself with CMake. -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[100%] Linking CXX static library libsdsl.a +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.21.12") Found Protobuf using FindProtobuf.cmake -- Found Threads: TRUE Using real Threads library -- Checking for module 'htslib' -- Found htslib, version 1.20 -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Checking for module 'jansson' -- Found jansson, version 2.14 Using installed libhandlegraph --- Configuring done (7.7s) --- Generating done (0.1s) +-- Configuring done (5.7s) +-- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -/usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make -f CMakeFiles/test_libvgio.dir/build.make CMakeFiles/test_libvgio.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -/usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/test_libvgio.dir/cmake_clean.cmake +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +/usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +/usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' @@ -3396,7 +3437,6 @@ make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' @@ -3408,108 +3448,94 @@ make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 2%] Running cpp protocol buffer compiler on deps/vg.proto -/usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto [ 5%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto +/usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -[ 8%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_emitter.cpp -[ 11%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" +[ 8%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o +[ 14%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o [ 14%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_io.cpp -[ 17%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -[ 20%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/vg.pb.cc.o -MF CMakeFiles/vgio_static.dir/vg.pb.cc.o.d -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/vg.pb.cc -[ 23%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o +[ 26%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o +[ 26%] Building CXX 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CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_emitter.cpp +[ 58%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[100%] Linking CXX static library libsdsl.a -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/simple_sds.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Built target sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 +[ 61%] 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -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 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/reproducible-path/vg-1.59.0+ds/include/sdsl/*' rm -f '/build/reproducible-path/vg-1.59.0+ds/lib/libsdsl*' +[ 64%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks +[ 67%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio.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 make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" +g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' +ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o [100%] Built target sdsl make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 +[ 70%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/edit.cpp.o -MF CMakeFiles/vgio.dir/src/edit.cpp.o.d -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/edit.cpp make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. @@ -3544,6 +3570,7 @@ -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sampling_strategy.hpp +ranlib sonLib.a -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_iterators.hpp @@ -3640,20 +3667,19 @@ A cheat sheet in the extras/cheatsheet-directory. Have fun! . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gcsa2 && make directories && make lib/libgcsa2.a && mv lib/libgcsa2.a /build/reproducible-path/vg-1.59.0+ds/lib -. ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwt && make clean && make && mv lib/libgbwt.a /build/reproducible-path/vg-1.59.0+ds/lib -. ./source_me.sh && rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/reproducible-path/vg-1.59.0+ds/include:/build/reproducible-path/vg-1.59.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" make && cp lib/libbdsg.a /build/reproducible-path/vg-1.59.0+ds/lib && cp -r bdsg/include/* /build/reproducible-path/vg-1.59.0+ds/include -rm -f lib/libxg.a -cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include -. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' +rm *.o +mv sonLib.a ../lib/ +gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' mkdir -p bin mkdir -p lib mkdir -p obj +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp +. ./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 make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' rm -rf bin lib obj -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C rm -f *.o *.a build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' @@ -3665,84 +3691,88 @@ mkdir -p lib mkdir -p obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/bwtmerge.o src/bwtmerge.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwt.o src/cached_gbwt.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dynamic_gbwt.o src/dynamic_gbwt.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/fast_locate.o src/fast_locate.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwt.o src/gbwt.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata.o src/metadata.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/test.o src/test.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/variants.o src/variants.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_gbwt.o src/build_gbwt.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_ri.o src/build_ri.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/merge_gbwt.o src/merge_gbwt.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/benchmark.o src/benchmark.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata_tool.o src/metadata_tool.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp -[ ! -e bdsg/obj ] || rm -r bdsg/obj +[ 73%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/hfile_cppstream.cpp +[ 76%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/json2pb.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dbg.o src/dbg.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp +gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm +[ 79%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_emitter.cpp +gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm +. ./source_me.sh && rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/reproducible-path/vg-1.59.0+ds/include:/build/reproducible-path/vg-1.59.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp" make && cp lib/libbdsg.a /build/reproducible-path/vg-1.59.0+ds/lib && cp -r bdsg/include/* /build/reproducible-path/vg-1.59.0+ds/include +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' +[ 82%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_iterator.cpp +[ ! -e bdsg/obj ] || rm -r bdsg/obj [ ! -e lib ] || rm -r lib -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gcsa.o src/gcsa.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/lcp.o src/lcp.cpp [ ! -e bin ] || rm -r bin -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_graph.o src/path_graph.cpp make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o +rm -f lib/libxg.a +cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include +mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest +. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp +gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 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-Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_graph.o src/path_graph.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwt.o src/cached_gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o -g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp -ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o -ranlib sonLib.a -rm *.o -mv sonLib.a ../lib/ -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dynamic_gbwt.o src/dynamic_gbwt.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/fast_locate.o src/fast_locate.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwt.o src/gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/reference_path_overlay.cpp -o bdsg/obj/reference_path_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/packed_reference_path_overlay.cpp -o bdsg/obj/packed_reference_path_overlay.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/path_subgraph_overlay.cpp -o bdsg/obj/path_subgraph_overlay.o -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/subgraph_overlay.cpp -o bdsg/obj/subgraph_overlay.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o -mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o -mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong 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-I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/variants.o src/variants.cpp [ 97%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. 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/usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +[ 97%] Built target vgio +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_gbwt.o src/build_gbwt.cpp +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-Wextra -DNDEBUG -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 +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/ranlib libvgio.a make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [100%] Built target vgio_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg --check-build-system CMakeFiles/Makefile.cmake 0 @@ -3750,6 +3780,8 @@ make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/benchmark.o src/benchmark.cpp make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' @@ -3761,21 +3793,33 @@ make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" -make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +[ 50%] Built target vgio +make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" +mv ../bin/sonLibTests.tmp ../bin/sonLibTests +make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' +cp sonLib_daemonize.py ./bin/sonLib_daemonize.py +chmod +x ./bin/sonLib_daemonize.py +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' +. ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/reproducible-path/vg-1.59.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/reproducible-path/vg-1.59.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/reproducible-path/vg-1.59.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' +cd externalTools && make all +make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' +cd threeEdgeConnected && make all +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' +gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -[ 50%] Built target vgio_static -[100%] Built target vgio +[100%] Built target vgio_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall @@ -3786,54 +3830,46 @@ /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libvgio.so +ar rc 3EdgeConnected.a *.o -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libvgio.a +ranlib 3EdgeConnected.a +rm *.o -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/vpkg.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_internal.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/fdstream.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_cppstream.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_input_stream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/loader.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_output_stream.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_emitter.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream_multiplexer.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_internal.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/loader.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_io.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/gafkluge.hpp +mv 3EdgeConnected.a ../..//../sonLib/lib/ +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/edit.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_cppstream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_iterator.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/basic_stream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_iterator.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/vpkg.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/json2pb.h --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_emitter.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/fdstream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/registry.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_emitter.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_emitter.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/gafkluge.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/edit.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_iterator.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/registry.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h +cp inc/*.h ../..//../sonLib/lib/ -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -mv ../bin/sonLibTests.tmp ../bin/sonLibTests -make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' -cp sonLib_daemonize.py ./bin/sonLib_daemonize.py -chmod +x ./bin/sonLib_daemonize.py -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' -. ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/reproducible-path/vg-1.59.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/reproducible-path/vg-1.59.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/reproducible-path/vg-1.59.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' -cd externalTools && make all -make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' -cd threeEdgeConnected && make all -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' -gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c -ar rc 3EdgeConnected.a *.o -ranlib 3EdgeConnected.a -rm *.o -mv 3EdgeConnected.a ../..//../sonLib/lib/ -cp inc/*.h ../..//../sonLib/lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata_tool.o src/metadata_tool.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -I inc -I .//../sonLib/lib/ -c impl/*.c @@ -3844,6 +3880,8 @@ mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' +ar rcs lib/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/libgbwt.a obj/algorithms.o obj/bwtmerge.o obj/cached_gbwt.o obj/dynamic_gbwt.o obj/fast_locate.o obj/files.o obj/gbwt.o obj/internal.o obj/metadata.o obj/support.o obj/test.o obj/utils.o obj/variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_gbwt obj/build_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_ri obj/build_ri.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 @@ -3878,8 +3916,6 @@ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa2gbwt.o src/gfa2gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz_stats.o src/gbz_stats.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/kmer_freq.o src/kmer_freq.cpp -ar rcs lib/libgcsa2.a obj/algorithms.o obj/dbg.o obj/files.o obj/gcsa.o obj/internal.o obj/lcp.o obj/path_graph.o obj/support.o obj/utils.o -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/mapped_structs.o bdsg/obj/packed_graph.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/reference_path_overlay.o bdsg/obj/packed_reference_path_overlay.o bdsg/obj/path_subgraph_overlay.o bdsg/obj/subgraph_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/snarl_distance_index.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a @@ -4329,8 +4365,8 @@ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from -'/nonexistent/first-build/lib' and -'/nonexistent/first-build/include' +'/nonexistent/second-build/lib' and +'/nonexistent/second-build/include' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl @@ -5485,7 +5521,7 @@ # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' - make -j42 "INSTALL=install --strip-program=true" SFX=-avx all test/build_graph bin/shuf + make -j20 "INSTALL=install --strip-program=true" SFX=-avx all test/build_graph bin/shuf make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC @@ -5500,75 +5536,52 @@ . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/reproducible-path/vg-1.59.0+ds/include" make libs && cp lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/lib/ && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS && cp src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp -r src/include/structures /build/reproducible-path/vg-1.59.0+ds/include/ rm -f lib/cleaned_old_protobuf* +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' +gcc -c -o ssw.o ssw.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -pipe -O3 -I. rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' -rm -f /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/* +g++ -c -o ssw_cpp.o ssw_cpp.cpp -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -pipe -O3 -I. +gcc -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c +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' -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g -c -o obj/gssw.o src/gssw.c -Library will be installed in '/build/reproducible-path/vg-1.59.0+ds' -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd externalTools && make all rm -Rf include/google/protobuf deps/protobuf -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' -gcc -c -o ssw.o ssw.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -pipe -O3 -I. -g++ -c -o ssw_cpp.o ssw_cpp.cpp -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -pipe -O3 -I. -gcc -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj; fi -make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' -cd cutest && make all -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o -cd quicktree_1.1 && make all CC="gcc -std=c99" -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o WARNING: .git/hooks directory does not exists. - The pre-commit hook is not installed. -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o -touch lib/cleaned_old_protobuf_v003 -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test; fi -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o if [ ! -d bin ]; then mkdir -p bin; fi -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o + The pre-commit hook is not installed. +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' if [ ! -d obj ]; then mkdir -p obj; fi -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin; fi -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib; fi -gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o +make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' +cd cutest && 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/* +cd quicktree_1.1 && make all CC="gcc -std=c99" if [ ! -d lib ]; then mkdir -p lib; fi -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps; fi -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o +touch lib/cleaned_old_protobuf_v003 find bin obj lib -type f -delete +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[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o -. ./source_me.sh && g++ -I -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/progress_bar.o deps/progress_bar/progress_bar.cpp gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o -g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' -if [ ! -d bin ]; then mkdir -p bin; fi -if [ ! -d obj ]; then mkdir -p obj; fi gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c -make[2]: 'bin/shuf' is up to date. -if [ ! -d lib ]; then mkdir -p lib; fi -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/union_find.cpp -o obj/union_find.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/stable_double.cpp -o obj/stable_double.o +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 +if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test; fi +if [ ! -d /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 /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib; fi +if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps; fi +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' +gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. @@ -5578,6 +5591,12 @@ to work with policies introduced by or earlier. +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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/union_find.cpp -o obj/union_find.o +. ./source_me.sh && g++ -I -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/progress_bar.o deps/progress_bar/progress_bar.cpp ./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); @@ -5607,10 +5626,6 @@ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: -/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] - 20 | } - | ^ ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); @@ -5618,40 +5633,26 @@ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o +g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp +make[2]: 'bin/shuf' is up to date. +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -c src/stable_double.cpp -o obj/stable_double.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o -- The C compiler identification is GNU 14.2.0 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o -- The CXX compiler identification is GNU 14.2.0 -- The C compiler identification is GNU 14.2.0 --- The CXX compiler identification is GNU 14.2.0 --- Detecting C compiler ABI info +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o -- The C compiler identification is GNU 14.2.0 --- Detecting CXX compiler ABI info -- The CXX compiler identification is GNU 14.2.0 --- Detecting C compiler ABI info -ar rc cuTest.a *.o -ranlib cuTest.a -rm -f *.o -mv cuTest.a ../../lib/ -cp CuTest.h ../../lib/ -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' --- Detecting C compiler ABI info - done -/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: -/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] - 96 | } - | ^ --- Check for working C compiler: /usr/bin/gcc - skipped --- Detecting C compile features --- Detecting C compile features - done -- Detecting CXX compiler ABI info --- Detecting CXX compiler ABI info - done --- Check for working CXX compiler: /usr/bin/g++ - skipped --- Detecting CXX compile features --- Detecting CXX compile features - done +ar rc cuTest.a *.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o -- Detecting C compiler ABI info --- Detecting C compiler ABI info - done --- Check for working C compiler: /usr/bin/gcc - skipped --- Detecting C compile features --- Detecting C compile features - done --- Detecting CXX compiler ABI info +ranlib cuTest.a src/gssw.c: In function ‘gssw_graph_print’: src/gssw.c:1947:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1947 | fprintf(stdout, "GRAPH // node %llu %u %s\n", n->id, n->len, n->seq); @@ -5700,7 +5701,10 @@ | | uint64_t {aka long unsigned int} | long long unsigned int | %lu +rm -f *.o +-- The CXX compiler identification is GNU 14.2.0 src/gssw.c: In function ‘gssw_print_graph_cigar’: +mv cuTest.a ../../lib/ 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); | ~~~^ ~~~~~~~~~~~~ @@ -5708,7 +5712,10 @@ | | uint64_t {aka long unsigned int} | long long unsigned int | %lu --- Detecting CXX compiler ABI info - done +cp CuTest.h ../../lib/ +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' +-- Detecting C compiler ABI info +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o 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); @@ -5718,6 +5725,7 @@ | long long unsigned int | %lu src/gssw.c: In function ‘gssw_create_seed_word’: +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o 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); | ~~~^ ~~~~~~~~~~~ @@ -5725,104 +5733,33 @@ | | uint64_t {aka long unsigned int} | long long unsigned int | %lu --- Detecting C compiler ABI info - done +/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 | } + | ^ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o +-- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done --- Configuring done (1.5s) +-- Detecting C compiler ABI info - done +-- Detecting C compiler ABI info - done +-- Detecting C compiler ABI info -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done --- Generating done (0.0s) --- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build --- Compiler is recent enough to support C++14. --- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' --- Detecting CXX compiler ABI info - done -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' --- Check for working CXX compiler: /usr/bin/g++ - skipped --- Detecting CXX compile features -[ 16%] Building CXX object 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CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_acyclic.cpp +-- Detecting CXX compiler ABI info +-- Check for working C compiler: /usr/bin/gcc - skipped +-- Detecting C compile features +-- Detecting C compile features - done +/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: +/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] + 96 | } + | ^ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm +-- Detecting CXX compiler ABI info 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 @@ -5831,105 +5768,158 @@ mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h -[ 85%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/split_strands.cpp cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h -[ 88%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o +-- Detecting CXX compiler ABI info - done cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/chop.cpp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp -mv ../lib/jsmn.h.tmp ../lib/jsmn.h --- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success +-- Detecting C compiler ABI info - done cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp +mv ../lib/jsmn.h.tmp ../lib/jsmn.h mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp +-- Check for working CXX compiler: /usr/bin/g++ - skipped +-- Detecting CXX compile features +-- Detecting CXX compile features - done mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp +-- Configuring done (2.6s) mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h +-- Generating done (0.0s) +-- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp +-- Check for working C compiler: /usr/bin/gcc - skipped +-- Detecting C compile features +-- Detecting C compile features - done mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp -mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp -cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp +mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +-- Detecting CXX compiler ABI info - done +-- Compiler is recent enough to support C++14. +-- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h +cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp -cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h +make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +-- Check for working CXX compiler: /usr/bin/g++ - skipped +-- Detecting CXX compile features +-- Detecting CXX compile features - done +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp -mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h +libhandlegraph is root project or external_project +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' cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp -mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h +mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h +-- Configuring done (2.8s) cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp -mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp +mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h +mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h +[ 16%] Building CXX object CMakeFiles/kff.dir/kff_io.cpp.o mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp -[ 91%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp -mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp +mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h +mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp -mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp -rm -f lib/libstructures.a +mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h -ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o cp inc/sonLibString.h ../lib/sonLibString.h.tmp -ar: creating lib/libstructures.a -mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp -mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp -cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp +mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h +-- Generating done (0.1s) +-- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build +mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h -mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h +cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp -mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +/usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 +mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/stGraph.h ../lib/stGraph.h.tmp +mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp -mv ../lib/stJson.h.tmp ../lib/stJson.h -[ 94%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o cp inc/stMatrix.h ../lib/stMatrix.h.tmp -mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/extend.cpp cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp -mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h +mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp +mv ../lib/stJson.h.tmp ../lib/stJson.h +mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h +/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 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 +make -f CMakeFiles/Makefile2 all cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp +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 mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h +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=" gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -I inc -I ../lib/ -c impl/*.c --- Performing Test HAVE_CXA_DEMANGLE +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +-- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG - Success +-- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS +[ 5%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o +[ 2%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o -c 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-std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp +[ 14%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o +[ 17%] 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=. 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CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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 +[ 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/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 +[ 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/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 gcc -o ssw_test ssw.o main.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -pipe -O3 -I. -lm -lz gcc -o example_c ssw.o example.c -I 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CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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 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] @@ -5952,15 +5942,8 @@ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ --- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success --- Could NOT find Git (missing: GIT_EXECUTABLE) -CMake Warning at CMakeLists.txt:102 (message): - git not found. 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valid for C++/ObjC++ but not for C +[ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o +[ 51%] 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_tips.cpp +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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 +-- Performing Test HAVE_CXA_DEMANGLE - Success +-- Compiler supports DEMANGLE. +-- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE +[ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong 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+ inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: +src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ + 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +-- Performing Test HAVE_GCC_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 +[ 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp +[ 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 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doxygen dot +-- Configuring done (7.5s) +[ 85%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/split_strands.cpp +[ 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 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CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/extend.cpp +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); + | ^~~~~~~~~~~ +-- Generating done (0.8s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 -make[3]: 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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 +[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp -[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o +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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF 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lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_isa.cpp -[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o +[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 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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 +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa.cpp +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 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 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/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/memory_management.cpp -[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp -[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include 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lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sd_vector.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sfstream.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o -MF CMakeFiles/sdsl.dir/simple_sds.cpp.o.d -o CMakeFiles/sdsl.dir/simple_sds.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/simple_sds.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/structure_tree.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint128_t.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/wt_helper.cpp -src/gssw.c: In function ‘gssw_sw_software_word’: -src/gssw.c:1117:5: warning: ‘__builtin_memcpy’ writing between 18446744069414584336 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] - 1117 | memcpy(scratch, to_unswizzle, size * sizeof(int16_t)); - | ^ -In function ‘unswizzle_word’, - inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: -src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ - 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/gssw.c: In function ‘gssw_node_create’: -src/gssw.c:4975:5: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - 4975 | strncpy(n->seq, seq, len); n->seq[len] = 0; - | ^ -src/gssw.c:4971:19: note: length computed here - 4971 | int32_t len = strlen(seq); - | ^~~~~~~~~~~ +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 33%] Linking CXX static library libkff.a In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/vector:63, @@ -6089,16 +6107,6 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from ‘void* operator new(std::size_t)’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[ 33%] Linking CXX static library libkff.a -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); @@ -6121,8 +6129,26 @@ /usr/include/lz4.h:774:68: note: declared here 774 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 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' +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 +[ 50%] Building CXX object CMakeFiles/kff_example.dir/main.cpp.o +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/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 +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/memory_management.cpp +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp +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' +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_fs.cpp 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); @@ -6132,17 +6158,7 @@ impl/sonLibConnectivity.c:608:9: note: call to ‘free’ here 608 | free(comp); | ^~~~~~~~~~ -[ 33%] Built target kff -ar rc /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[ 50%] Building CXX object benchmarks/CMakeFiles/reader_bench.dir/reader.cpp.o -[ 66%] Building CXX object CMakeFiles/kff_example.dir/main.cpp.o In file included from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: @@ -6155,35 +6171,55 @@ /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:448:9: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 448 | *word &= | ^~~~~ -ranlib /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +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' +[ 66%] Building CXX object benchmarks/CMakeFiles/reader_bench.dir/reader.cpp.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp +[ 83%] Linking CXX executable kff_example +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sd_vector.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[ 83%] Linking CXX executable reader_bench +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sfstream.cpp +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +[ 83%] Built target kff_example # Make dest directory -gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz -gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz -ar rvs lib/libgssw.a obj/gssw.o -ar: creating lib/libgssw.a -a - obj/gssw.o -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -[ 83%] Built target reader_bench +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/structure_tree.cpp +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[100%] Linking CXX executable kff_example +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint128_t.cpp +[100%] Linking CXX executable reader_bench +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -[100%] Built target kff_example +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/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%] Built target reader_bench +gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz 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' +gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz +ar rvs lib/libgssw.a obj/gssw.o +ar: creating lib/libgssw.a +a - obj/gssw.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C @@ -6196,19 +6232,21 @@ impl/sonLibTreap.c:329:9: note: call to ‘free’ here 329 | free(rmnode); | ^~~~~~~~~~~~ +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 94%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +make[5]: 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' [ 97%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 @@ -6216,15 +6254,16 @@ /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/g++ -fPIC -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,--dependency-file,CMakeFiles/handlegraph_shared.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Built target handlegraph_shared /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Built target handlegraph_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' @@ -6248,72 +6287,72 @@ 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 -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -make[5]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. +make[5]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build +make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -make[5]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. +make[5]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -[ 97%] Built target handlegraph_static [100%] Built target handlegraph_shared +[100%] Built target handlegraph_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.a -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_deletable_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_metadata.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_metadata.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_position_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/deletable_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/util.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/buildable_snarl_decomposition.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/trivially_serializable.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/iteratee.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_handle_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_metadata.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/types.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/snarl_decomposition.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/named_node_back_translation.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_metadata.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_tips.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/count_walks.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/split_strands.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/eades_algorithm.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/are_equivalent.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dijkstra.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/append_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/apply_orientations.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal/dfs.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dagify.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/reverse_complement.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_shortest_paths.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/topological_sort.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/copy_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/strongly_connected_components.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/chop.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/extend.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/weakly_connected_components.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_single_stranded.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/chop.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_shortest_paths.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/are_equivalent.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_acyclic.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/snarl_decomposition.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/types.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/named_node_back_translation.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dijkstra.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/append_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/apply_orientations.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_single_stranded.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/count_walks.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/weakly_connected_components.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/eades_algorithm.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/topological_sort.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/copy_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_tips.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dagify.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/expanding_overlay_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/trivially_serializable.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/iteratee.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_handle_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_mutable_handle_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_position_handle_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphConfig.cmake @@ -6322,15 +6361,12 @@ rm -f /build/reproducible-path/vg-1.59.0+ds/include/vg.pb.h /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp" && export LDFLAGS="-Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && rm -rf build-vg && mkdir build-vg && cd build-vg && PKG_CONFIG_PATH=/build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig: cmake -DCMAKE_CXX_STANDARD=14 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH="/usr;/" -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make clean && VERBOSE=1 make && make install -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") Building libvgio for C++ 14 @@ -6346,7 +6382,8 @@ -- Checking for module 'jansson' -- Found jansson, version 2.14 Using installed libhandlegraph --- Configuring done (1.1s) +-- Configuring done (2.0s) +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- 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' @@ -6361,9 +6398,9 @@ make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +/usr/bin/cmake -P CMakeFiles/test_libvgio.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake -/usr/bin/cmake -P CMakeFiles/test_libvgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' @@ -6389,96 +6426,86 @@ make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 2%] Running cpp protocol buffer compiler on deps/vg.proto -/usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto [ 5%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto +/usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build +make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -[ 8%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -[ 14%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -[ 14%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -[ 20%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -[ 20%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/basic_stream.cpp +[ 8%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o +[ 11%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o +[ 20%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o +[ 20%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o +[ 20%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o +[ 23%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o +[ 26%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_emitter.cpp -[ 23%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg 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/build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/vg.pb.cc.o -MF CMakeFiles/vgio_static.dir/vg.pb.cc.o.d -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/vg.pb.cc -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection 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/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp +[ 58%] Building CXX object CMakeFiles/vgio.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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/basic_stream.cpp +/usr/bin/g++ -Dvgio_EXPORTS 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/build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/stream.cpp.o -MF CMakeFiles/vgio.dir/src/stream.cpp.o.d -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream.cpp -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection 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cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o +[ 61%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o +/usr/bin/g++ 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-I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 +[ 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 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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 +[ 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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 gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm +[ 82%] 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/simple_sds.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' +gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm [100%] Built target sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 @@ -6490,15 +6517,17 @@ make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks -mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" -mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest +mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest +gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build +[ 85%] 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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 make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' @@ -6511,6 +6540,7 @@ make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake +mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest -- Install configuration: "Release" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vector_il.hpp @@ -6568,6 +6598,8 @@ -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_vlc.hpp +[ 88%] Building CXX 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -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 -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/memory_management.hpp @@ -6625,6 +6657,7 @@ -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libsdsl.a +mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/reproducible-path/vg-1.59.0+ds/include'. @@ -6635,34 +6668,28 @@ A cheat sheet in the extras/cheatsheet-directory. Have fun! . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gcsa2 && make directories && make lib/libgcsa2.a && mv lib/libgcsa2.a /build/reproducible-path/vg-1.59.0+ds/lib -. ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwt && make clean && make && mv lib/libgbwt.a /build/reproducible-path/vg-1.59.0+ds/lib -. ./source_me.sh && rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/reproducible-path/vg-1.59.0+ds/include:/build/reproducible-path/vg-1.59.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp" make && cp lib/libbdsg.a /build/reproducible-path/vg-1.59.0+ds/lib && cp -r bdsg/include/* /build/reproducible-path/vg-1.59.0+ds/include -rm -f lib/libxg.a -cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include -. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp +[ 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 -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/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 make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' mkdir -p bin mkdir -p lib -rm -rf bin lib obj mkdir -p obj make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' -rm -f *.o *.a build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' -[ ! -e bdsg/obj ] || rm -r bdsg/obj -cd tests && make clean /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp -make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' +[ 94%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio_static.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/vpkg.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dbg.o src/dbg.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gcsa.o src/gcsa.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/lcp.o src/lcp.cpp +. ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwt && make clean && make && mv lib/libgbwt.a /build/reproducible-path/vg-1.59.0+ds/lib +. ./source_me.sh && rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/reproducible-path/vg-1.59.0+ds/include:/build/reproducible-path/vg-1.59.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp" make && cp lib/libbdsg.a /build/reproducible-path/vg-1.59.0+ds/lib && cp -r bdsg/include/* /build/reproducible-path/vg-1.59.0+ds/include +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' +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 -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_graph.o src/path_graph.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp +[ ! -e bdsg/obj ] || rm -r bdsg/obj make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' @@ -6670,45 +6697,29 @@ mkdir -p lib mkdir -p obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/bwtmerge.o src/bwtmerge.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwt.o src/cached_gbwt.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dynamic_gbwt.o src/dynamic_gbwt.cpp [ ! -e lib ] || rm -r lib -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/fast_locate.o src/fast_locate.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwt.o src/gbwt.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata.o src/metadata.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/test.o src/test.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/variants.o src/variants.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_gbwt.o src/build_gbwt.cpp [ ! -e bin ] || rm -r bin make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' +rm -f lib/libxg.a +cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include +. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_ri.o src/build_ri.cpp -mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/merge_gbwt.o src/merge_gbwt.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/benchmark.o src/benchmark.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata_tool.o src/metadata_tool.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/mapped_structs.cpp -o bdsg/obj/mapped_structs.o +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/bwtmerge.o src/bwtmerge.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwt.o src/cached_gbwt.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dynamic_gbwt.o src/dynamic_gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/reference_path_overlay.cpp -o bdsg/obj/reference_path_overlay.o +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/fast_locate.o src/fast_locate.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/packed_reference_path_overlay.cpp -o bdsg/obj/packed_reference_path_overlay.o +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/path_subgraph_overlay.cpp -o bdsg/obj/path_subgraph_overlay.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/subgraph_overlay.cpp -o bdsg/obj/subgraph_overlay.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o mv ../bin/sonLibTests.tmp ../bin/sonLibTests make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py @@ -6721,28 +6732,44 @@ cd threeEdgeConnected && make all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwt.o src/gbwt.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp ar rc 3EdgeConnected.a *.o ranlib 3EdgeConnected.a rm *.o mv 3EdgeConnected.a ../..//../sonLib/lib/ cp inc/*.h ../..//../sonLib/lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/subgraph_overlay.cpp -o bdsg/obj/subgraph_overlay.o +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gcsa.o src/gcsa.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -I inc -I .//../sonLib/lib/ -c impl/*.c +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o +ar rc stPinchesAndCacti.a *.o +ranlib stPinchesAndCacti.a +[ 97%] Linking CXX shared library libvgio.so +/usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 +rm *.o +mv stPinchesAndCacti.a .//../sonLib/lib/ +cp inc/*.h .//../sonLib/lib/ gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a -[ 97%] Linking CXX static library libvgio.a +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata.o src/metadata.cpp +[100%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake +/usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wl,--dependency-file,CMakeFiles/vgio.dir/link.d -Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp +[100%] 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 -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/ranlib libvgio.a make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -[ 97%] Built target vgio_static -[100%] Linking CXX shared library libvgio.so -/usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 -/usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wl,--dependency-file,CMakeFiles/vgio.dir/link.d -Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -[100%] Built target vgio +[100%] Built target vgio_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' @@ -6761,17 +6788,19 @@ make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 0%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend -make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 50%] Built target vgio +make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/test.o src/test.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' @@ -6786,44 +6815,51 @@ make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' Install the project... /usr/bin/cmake -P cmake_install.cmake -ar rc stPinchesAndCacti.a *.o -ranlib stPinchesAndCacti.a -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libvgio.so -rm *.o -mv stPinchesAndCacti.a .//../sonLib/lib/ -cp inc/*.h .//../sonLib/lib/ -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libvgio.a -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/vg -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/vpkg.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_internal.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/fdstream.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_cppstream.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_input_stream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/loader.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_output_stream.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_emitter.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream_multiplexer.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_internal.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/loader.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_io.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/gafkluge.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/edit.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_cppstream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_iterator.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/basic_stream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_iterator.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/vpkg.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/json2pb.h --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_emitter.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/fdstream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/registry.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_emitter.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_emitter.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/gafkluge.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/edit.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_iterator.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/registry.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/variants.o src/variants.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_gbwt.o src/build_gbwt.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_ri.o src/build_ri.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/lcp.o src/lcp.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_graph.o src/path_graph.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/merge_gbwt.o src/merge_gbwt.cpp make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/benchmark.o src/benchmark.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata_tool.o src/metadata_tool.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp ar rcs lib/libgbwt.a obj/algorithms.o obj/bwtmerge.o obj/cached_gbwt.o obj/dynamic_gbwt.o obj/fast_locate.o obj/files.o obj/gbwt.o obj/internal.o obj/metadata.o obj/support.o obj/test.o obj/utils.o obj/variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_gbwt obj/build_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_ri obj/build_ri.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 @@ -6858,12 +6894,12 @@ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa2gbwt.o src/gfa2gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz_stats.o src/gbz_stats.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/kmer_freq.o src/kmer_freq.cpp -ar rcs lib/libgcsa2.a obj/algorithms.o obj/dbg.o obj/files.o obj/gcsa.o obj/internal.o obj/lcp.o obj/path_graph.o obj/support.o obj/utils.o -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/mapped_structs.o bdsg/obj/packed_graph.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/reference_path_overlay.o bdsg/obj/packed_reference_path_overlay.o bdsg/obj/path_subgraph_overlay.o bdsg/obj/subgraph_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/snarl_distance_index.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' +ar rcs lib/libgcsa2.a obj/algorithms.o obj/dbg.o obj/files.o obj/gcsa.o obj/internal.o obj/lcp.o obj/path_graph.o obj/support.o obj/utils.o +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a ar rcs lib/libgbwtgraph.a obj/algorithms.o obj/cached_gbwtgraph.o obj/gbwtgraph.o obj/gbz.o obj/gfa.o obj/internal.o obj/minimizer.o obj/path_cover.o obj/utils.o @@ -7173,8 +7209,6 @@ . ./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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/haplotypes_main.o src/subcommand/haplotypes_main.cpp -. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp -. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:147:31: required from here @@ -7190,6 +7224,8 @@ /usr/include/google/protobuf/message_lite.h:381:7: note: declared here 381 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ +. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp +. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp @@ -7309,8 +7345,8 @@ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from -'/nonexistent/first-build/lib' and -'/nonexistent/first-build/include' +'/nonexistent/second-build/lib' and +'/nonexistent/second-build/include' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl @@ -8465,7 +8501,7 @@ # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' - make -j42 "INSTALL=install --strip-program=true" SFX=-sse4.1 all test/build_graph bin/shuf + make -j20 "INSTALL=install --strip-program=true" SFX=-sse4.1 all test/build_graph bin/shuf make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC @@ -8482,70 +8518,51 @@ rm -f lib/cleaned_old_protobuf* make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' gcc -c -o ssw.o ssw.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -pipe -O3 -I. +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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -pipe -O3 -I. gcc -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c -Library will be installed in '/build/reproducible-path/vg-1.59.0+ds' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' -rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc -gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd externalTools && make all +gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c +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 -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -WARNING: .git/hooks directory does not exists. - The pre-commit hook is not installed. -if [ ! -d obj ]; then mkdir -p obj; fi -rm -f /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/* -rm -Rf include/google/protobuf deps/protobuf -if [ ! -d lib ]; then mkdir -p lib; fi make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make all +rm -f /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/* +if [ ! -d obj ]; then mkdir -p obj; fi cd quicktree_1.1 && make all CC="gcc -std=c99" -touch lib/cleaned_old_protobuf_v003 -find bin obj lib -type f -delete +rm -Rf include/google/protobuf deps/protobuf +Library will be installed in '/build/reproducible-path/vg-1.59.0+ds' +if [ ! -d lib ]; then mkdir -p lib; 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]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c +gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c +find bin obj lib -type f -delete gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c -if [ ! -d bin ]; then mkdir -p bin; fi -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj; fi gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c -gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c +touch lib/cleaned_old_protobuf_v003 gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c -if [ ! -d obj ]; then mkdir -p obj; fi -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o +WARNING: .git/hooks directory does not exists. + The pre-commit hook is not installed. +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -if [ ! -d lib ]; then mkdir -p lib; fi -. ./source_me.sh && g++ -I -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/progress_bar.o deps/progress_bar/progress_bar.cpp -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test; fi -g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o +if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj; fi gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/union_find.cpp -o obj/union_find.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o +if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test; fi +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' +if [ ! -d bin ]; then mkdir -p bin; fi +if [ ! -d obj ]; then mkdir -p obj; fi +if [ ! -d lib ]; then mkdir -p lib; fi if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin; fi -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib; fi -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps; fi -make[2]: 'bin/shuf' is up to date. -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. @@ -8555,9 +8572,10 @@ to work with policies introduced by or earlier. -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/union_find.cpp -o obj/union_find.o +if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib; fi +if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps; fi +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o ./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 ); @@ -8651,7 +8669,6 @@ | long long unsigned int | %lu src/gssw.c: In function ‘gssw_create_seed_byte’: --- The C compiler identification is GNU 14.2.0 src/gssw.c:5095:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5095 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); | ~~~^ ~~~~~~~~~~~ @@ -8667,198 +8684,202 @@ | | uint64_t {aka long unsigned int} | long long unsigned int | %lu -/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: -/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] - 20 | } - | ^ --- The C compiler identification is GNU 14.2.0 --- The CXX compiler identification is GNU 14.2.0 -/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: -/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] - 96 | } - | ^ +. ./source_me.sh && g++ -I -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/progress_bar.o deps/progress_bar/progress_bar.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o +g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o +make[2]: 'bin/shuf' is up to date. +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o ar rc cuTest.a *.o --- The CXX compiler identification is GNU 14.2.0 --- The CXX compiler identification is GNU 14.2.0 --- Detecting C compiler ABI info --- Detecting C compiler ABI info ranlib cuTest.a +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o +-- The C compiler identification is GNU 14.2.0 +-- The CXX compiler identification is GNU 14.2.0 -- The C compiler identification is GNU 14.2.0 --- Detecting CXX compiler ABI info rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' --- Detecting C compiler ABI info - done --- Detecting C compiler ABI info - done --- Detecting CXX compiler ABI info - done --- Check for working C compiler: /usr/bin/gcc - skipped --- Check for working C compiler: /usr/bin/gcc - skipped --- Detecting C compile features --- Detecting C compile features --- Detecting C compile features - done --- Detecting C compile features - done -gcc -o ssw_test ssw.o main.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -pipe -O3 -I. -lm -lz -gcc -o example_c ssw.o example.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -pipe -O3 -I. -lm -lz --- Check for working CXX compiler: /usr/bin/g++ - skipped --- Detecting CXX compile features --- Detecting CXX compile features - done --- Detecting CXX compiler ABI info +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o +/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 | } + | ^ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o +-- The C compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info --- Detecting C compiler ABI info +-- The CXX compiler identification is GNU 14.2.0 +-- The CXX compiler identification is GNU 14.2.0 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm -g++ -o example_cpp example.cpp ssw.o ssw_cpp.o -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -pipe -O3 -I. -lm -lz -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o +-- Detecting C compiler ABI info +-- Detecting C compiler ABI info +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp cp inc/bioioC.h ../lib/bioioC.h.tmp -cp inc/commonC.h ../lib/commonC.h.tmp -cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp -cp inc/hashTableC.h ../lib/hashTableC.h.tmp -cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h +gcc -o ssw_test ssw.o main.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -pipe -O3 -I. -lm -lz mv ../lib/bioioC.h.tmp ../lib/bioioC.h +cp inc/commonC.h ../lib/commonC.h.tmp +cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h +cp inc/hashTableC.h ../lib/hashTableC.h.tmp +gcc -o example_c ssw.o example.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -pipe -O3 -I. -lm -lz mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h +cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp +mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp +mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp +mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp -mv ../lib/jsmn.h.tmp ../lib/jsmn.h -mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h -mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp -cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h -cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp +cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h -cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp -cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp +cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h +cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h +/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 | } + | ^ +cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h +g++ -o example_cpp example.cpp ssw.o ssw_cpp.o -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -pipe -O3 -I. -lm -lz cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp -mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h -cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp +src/gssw.c: In function ‘gssw_sw_software_byte’: +src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] + 277 | memcpy(scratch, to_unswizzle, size); + | ^ +In function ‘unswizzle_byte’, + inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: +src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ + 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h -mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h +cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp +-- Detecting CXX compiler ABI info - done cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp -cp inc/sonLibList.h ../lib/sonLibList.h.tmp +mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h -cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp +cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h +cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp -mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h +-- Check for working CXX compiler: /usr/bin/g++ - skipped +-- Detecting CXX compile features +-- Detecting CXX compile features - done cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp -cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp -cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp +rm -f lib/libstructures.a +mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h +ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o +cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp +cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp +ar: creating lib/libstructures.a +cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h +cp inc/sonLibTreap.h ../lib/sonLibTreap.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 +-- Detecting C compiler ABI info - done +mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h +-- Detecting C compiler ABI info - done cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp -cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp -mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h -mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h +cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp cp inc/stGraph.h ../lib/stGraph.h.tmp cp inc/stJson.h ../lib/stJson.h.tmp +mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h +mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp -cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h -mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h -mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h +cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp -cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp +mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h -mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h +cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp +mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -rm -f lib/libstructures.a -ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o --- Detecting C compiler ABI info - done -ar: creating lib/libstructures.a -- Check for working C compiler: /usr/bin/gcc - skipped +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' -- Detecting C compile features -- Detecting C compile features - done -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' --- Detecting CXX compiler ABI info - done +-- Detecting C compiler ABI info +-- Check for working C compiler: /usr/bin/gcc - skipped +-- Detecting C compile features +-- Detecting C compile features - done +-- Detecting CXX compiler ABI info +-- Detecting CXX compiler ABI info +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 +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)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +-- Detecting C compiler ABI info - done -- Detecting CXX compiler ABI info - done +-- Check for working C compiler: /usr/bin/gcc - skipped +-- Detecting C compile features +-- Detecting C compile features - done -- Compiler is recent enough to support C++14. -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG -src/gssw.c: In function ‘gssw_sw_software_byte’: -src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] - 277 | memcpy(scratch, to_unswizzle, size); - | ^ -In function ‘unswizzle_byte’, - inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: -src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ - 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done --- Check for working CXX compiler: /usr/bin/g++ - skipped --- Detecting CXX compile features --- Detecting CXX compile features - done -libhandlegraph is root project or external_project --- Configuring done (2.1s) +-- Configuring done (4.1s) -- Generating done (0.0s) -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' -ar: creating /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a --- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -/usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 --- Configuring done (2.4s) -/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 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Detecting CXX compiler ABI info - done impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ -[ 20%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ -[ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { @@ -8866,7 +8887,6 @@ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ -[ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { @@ -8874,211 +8894,184 @@ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ -[ 28%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -MF 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 +-- Check for working CXX compiler: /usr/bin/g++ - skipped +-- Detecting CXX compile features +-- Detecting CXX compile features - done +make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +libhandlegraph is root project or external_project +[ 16%] Building CXX object CMakeFiles/kff.dir/kff_io.cpp.o +-- Configuring done (4.7s) +-- Generating done (0.1s) +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); + | ^~~~~~~~~~~ +-- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +/usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 +-- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG - Success +-- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS +/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks +make -f CMakeFiles/Makefile2 all +make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +[ 5%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o +[ 5%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o +[ 8%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o +[ 14%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o +[ 14%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o +[ 17%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o +[ 20%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o +[ 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 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its length [-Wstringop-truncation] - 4975 | strncpy(n->seq, seq, len); n->seq[len] = 0; - | ^ -src/gssw.c:4971:19: note: length computed here - 4971 | int32_t len = strlen(seq); - | ^~~~~~~~~~~ -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE +[ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c 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-std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/reverse_complement.cpp -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success +[ 85%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/split_strands.cpp -- 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 +[ 88%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/chop.cpp +[ 91%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/vector:63, - from /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:8: -In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = long int]’, - inlined from ‘static void std::allocator_traits >::deallocate(allocator_type&, pointer, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:544:23, - inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:389:19, - inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:368:15, - inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:738:7, - inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:445:5: -/usr/include/c++/14/bits/new_allocator.h:172:33: warning: ‘void operator delete(void*, std::size_t)’ called on pointer ‘’ with nonzero offset [1, 9223372036854775800] [-Wfree-nonheap-object] - 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); - | ^ -In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = long int]’, - inlined from ‘static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:509:28, - inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:380:33, - inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:398:44, - inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:334:26, - inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const value_type&, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:571:47, - inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:327:85: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from ‘void* operator new(std::size_t)’ - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ +[ 94%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/extend.cpp -- Looking for C++ include cstdio - found +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot +-- Configuring done (10.8s) cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C --- Configuring done (6.3s) cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C --- Generating done (0.5s) +-- Generating done (0.7s) -- 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 +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 8 +# Make dest directory +gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz +gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all +gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz +ar rvs lib/libgssw.a obj/gssw.o 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 +ar: creating lib/libgssw.a +a - obj/gssw.o make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' -[ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -[ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o -[ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -[ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o -[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_config.cpp -[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bits.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp +[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o +[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp -[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o +[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o +[ 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp +[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o +[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/config.cpp -[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_config.cpp +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/construct_isa.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_isa.cpp -[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o +[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/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 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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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 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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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/io.cpp +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 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-Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall 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/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_fs.cpp -[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sd_vector.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sfstream.cpp -[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o -MF CMakeFiles/sdsl.dir/simple_sds.cpp.o.d -o CMakeFiles/sdsl.dir/simple_sds.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/simple_sds.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/structure_tree.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint128_t.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/wt_helper.cpp -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[ 33%] Linking CXX static library libkff.a -ar rc /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] @@ -9102,26 +9095,42 @@ /usr/include/lz4.h:774:68: note: declared here 774 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -ranlib /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a -# Make dest directory -gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz -gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz +[ 33%] Linking CXX static library libkff.a +In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/vector:63, + from /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:8: +In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = long int]’, + inlined from ‘static void std::allocator_traits >::deallocate(allocator_type&, pointer, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:544:23, + inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:389:19, + inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:368:15, + inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:738:7, + inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:445:5: +/usr/include/c++/14/bits/new_allocator.h:172:33: warning: ‘void operator delete(void*, std::size_t)’ called on pointer ‘’ with nonzero offset [1, 9223372036854775800] [-Wfree-nonheap-object] + 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); + | ^ +In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = long int]’, + inlined from ‘static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:509:28, + inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:380:33, + inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:398:44, + inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:334:26, + inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const value_type&, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:571:47, + inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:327:85: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from ‘void* operator new(std::size_t)’ + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +ar rc /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz -ar rvs lib/libgssw.a obj/gssw.o -ar: creating lib/libgssw.a -a - obj/gssw.o +ranlib /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 33%] Built target kff make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -[ 50%] Building CXX object benchmarks/CMakeFiles/reader_bench.dir/reader.cpp.o -[ 66%] Building CXX object CMakeFiles/kff_example.dir/main.cpp.o +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' +[ 50%] Building CXX object CMakeFiles/kff_example.dir/main.cpp.o +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/memory_management.cpp 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); @@ -9131,11 +9140,31 @@ impl/sonLibConnectivity.c:608:9: note: call to ‘free’ here 608 | free(comp); | ^~~~~~~~~~ -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[ 83%] Linking CXX executable reader_bench +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_fs.cpp +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sd_vector.cpp +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sfstream.cpp +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o -MF CMakeFiles/sdsl.dir/simple_sds.cpp.o.d -o CMakeFiles/sdsl.dir/simple_sds.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/simple_sds.cpp +cc1: warning: command-line option ‘-std=c++14’ is valid 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 +[ 66%] Linking CXX executable kff_example +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: @@ -9148,23 +9177,41 @@ /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:448:9: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 448 | *word &= | ^~~~~ -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/structure_tree.cpp +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -[ 83%] Built target reader_bench +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint128_t.cpp +[ 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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/wt_helper.cpp +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[100%] Linking CXX executable reader_bench cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[100%] Linking CXX executable kff_example make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -[100%] Built target kff_example +[100%] Built target reader_bench make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +impl/sonLibTreap.c: In function ‘stTreap_remove’: +impl/sonLibTreap.c:331:18: warning: pointer ‘rmnode’ used after ‘free’ [-Wuse-after-free] + 331 | stTreap *p = rmnode->parent; + | ^ +impl/sonLibTreap.c:329:9: note: call to ‘free’ here + 329 | free(rmnode); + | ^~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' @@ -9179,25 +9226,19 @@ make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build -make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +make -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' [ 97%] Linking CXX shared library libhandlegraph.so -[100%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 +[100%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/g++ -fPIC -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,--dependency-file,CMakeFiles/handlegraph_shared.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Built target handlegraph_shared -impl/sonLibTreap.c: In function ‘stTreap_remove’: -impl/sonLibTreap.c:331:18: warning: pointer ‘rmnode’ used after ‘free’ [-Wuse-after-free] - 331 | stTreap *p = rmnode->parent; - | ^ -impl/sonLibTreap.c:329:9: note: call to ‘free’ here - 329 | free(rmnode); - | ^~~~~~~~~~~~ /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' @@ -9207,13 +9248,13 @@ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' @@ -9237,7 +9278,6 @@ make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Built target handlegraph_shared make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 @@ -9251,48 +9291,48 @@ -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.a -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_deletable_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_metadata.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_metadata.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_position_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/deletable_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/util.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/buildable_snarl_decomposition.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/trivially_serializable.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/iteratee.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_handle_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_metadata.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/types.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/snarl_decomposition.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/named_node_back_translation.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_metadata.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_tips.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/count_walks.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/split_strands.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/eades_algorithm.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/are_equivalent.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dijkstra.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/append_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/apply_orientations.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal/dfs.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dagify.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/reverse_complement.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_shortest_paths.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/topological_sort.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/copy_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/strongly_connected_components.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/chop.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/extend.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/weakly_connected_components.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_single_stranded.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/chop.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_shortest_paths.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/are_equivalent.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_acyclic.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/snarl_decomposition.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/types.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/named_node_back_translation.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dijkstra.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/append_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/apply_orientations.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_single_stranded.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/count_walks.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/weakly_connected_components.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/eades_algorithm.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/topological_sort.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/copy_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_tips.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dagify.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/expanding_overlay_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/trivially_serializable.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/iteratee.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_handle_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_mutable_handle_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_position_handle_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphConfig.cmake @@ -9301,25 +9341,19 @@ rm -f /build/reproducible-path/vg-1.59.0+ds/include/vg.pb.h /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp" && export LDFLAGS="-Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && rm -rf build-vg && mkdir build-vg && cd build-vg && PKG_CONFIG_PATH=/build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig: cmake -DCMAKE_CXX_STANDARD=14 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH="/usr;/" -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make clean && VERBOSE=1 make && make install -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") Building libvgio for C++ 14 -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Could NOT find Protobuf (missing: Protobuf_DIR) No installed Protobuf has registered itself with CMake. -[100%] Linking CXX static library libsdsl.a -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.21.12") Found Protobuf using FindProtobuf.cmake -- Found Threads: TRUE @@ -9328,8 +9362,9 @@ -- Found htslib, version 1.20 -- Checking for module 'jansson' -- Found jansson, version 2.14 +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C Using installed libhandlegraph --- Configuring done (1.2s) +-- Configuring done (2.1s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' @@ -9355,6 +9390,7 @@ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg --check-build-system CMakeFiles/Makefile.cmake 0 +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' @@ -9371,81 +9407,91 @@ make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -[ 2%] Running cpp protocol buffer compiler on deps/vg.proto +[ 5%] Running cpp protocol buffer compiler on deps/vg.proto [ 5%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build +make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -[ 11%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -[ 8%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o -[ 17%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o -[ 17%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o -[ 20%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/hfile_cppstream.cpp -[ 23%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o -[ 26%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/basic_stream.cpp -/usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/simple_sds.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o -/usr/bin/ranlib libsdsl.a -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/edit.cpp.o -MF CMakeFiles/vgio.dir/src/edit.cpp.o.d -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/edit.cpp -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_emitter.cpp -[ 29%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_iterator.cpp -[ 35%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o -[ 35%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/registry.cpp.o -MF CMakeFiles/vgio.dir/src/registry.cpp.o.d -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/registry.cpp -[ 38%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/vg.pb.cc.o -MF CMakeFiles/vgio.dir/vg.pb.cc.o.d -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/vg.pb.cc -[ 44%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o -[ 44%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong 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CMakeFiles/vgio.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_io.cpp -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c 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CMakeFiles/vgio.dir/src/stream.cpp.o -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/json2pb.cpp -[ 50%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include 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-Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream_multiplexer.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" -/usr/bin/g++ 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CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp +[ 67%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o 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cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 +[ 76%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/json2pb.cpp +[ 79%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_emitter.cpp +[ 82%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_iterator.cpp +[ 85%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/registry.cpp.o -MF CMakeFiles/vgio.dir/src/registry.cpp.o.d -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/registry.cpp +/usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/simple_sds.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o +/usr/bin/ranlib libsdsl.a +make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 @@ -9462,6 +9508,10 @@ make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" +[ 88%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/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 +[ 91%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream_multiplexer.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' @@ -9590,6 +9640,8 @@ -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libsdsl.a +[ 94%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -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]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/reproducible-path/vg-1.59.0+ds/include'. @@ -9602,123 +9654,80 @@ . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gcsa2 && make directories && make lib/libgcsa2.a && mv lib/libgcsa2.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwt && make clean && make && mv lib/libgbwt.a /build/reproducible-path/vg-1.59.0+ds/lib . ./source_me.sh && rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/reproducible-path/vg-1.59.0+ds/include:/build/reproducible-path/vg-1.59.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp" make && cp lib/libbdsg.a /build/reproducible-path/vg-1.59.0+ds/lib && cp -r bdsg/include/* /build/reproducible-path/vg-1.59.0+ds/include -rm -f lib/libxg.a -cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include -. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' -mkdir -p bin -mkdir -p lib rm -rf bin lib obj -mkdir -p obj rm -f *.o *.a build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' -[ ! -e bdsg/obj ] || rm -r bdsg/obj -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' cd tests && make clean +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dbg.o src/dbg.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' +mkdir -p bin rm -f test_bwtmerge test_metadata test_queries test_support test_variants *.o -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gcsa.o src/gcsa.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/lcp.o src/lcp.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_graph.o src/path_graph.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' -[ ! -e lib ] || rm -r lib +mkdir -p lib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' +mkdir -p obj mkdir -p bin +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' mkdir -p lib mkdir -p obj +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' +[ ! -e bdsg/obj ] || rm -r bdsg/obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp +[ ! -e lib ] || rm -r lib [ ! -e bin ] || rm -r bin make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/bwtmerge.o src/bwtmerge.cpp make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwt.o src/cached_gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dynamic_gbwt.o src/dynamic_gbwt.cpp -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/fast_locate.o src/fast_locate.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dbg.o src/dbg.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gcsa.o src/gcsa.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/bwtmerge.o src/bwtmerge.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/lcp.o src/lcp.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_graph.o src/path_graph.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp -ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o -ranlib sonLib.a -rm *.o -mv sonLib.a ../lib/ -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwt.o src/gbwt.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata.o src/metadata.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwt.o src/cached_gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/mapped_structs.cpp -o bdsg/obj/mapped_structs.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/test.o src/test.cpp -mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp -mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o -mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/variants.o src/variants.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_gbwt.o src/build_gbwt.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_ri.o src/build_ri.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/merge_gbwt.o src/merge_gbwt.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/benchmark.o src/benchmark.cpp +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' +rm -f lib/libxg.a +cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include +. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/reference_path_overlay.cpp -o bdsg/obj/reference_path_overlay.o -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata_tool.o src/metadata_tool.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/packed_reference_path_overlay.cpp -o bdsg/obj/packed_reference_path_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/path_subgraph_overlay.cpp -o bdsg/obj/path_subgraph_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/subgraph_overlay.cpp -o bdsg/obj/subgraph_overlay.o +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dynamic_gbwt.o src/dynamic_gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o -mv ../bin/sonLibTests.tmp ../bin/sonLibTests -make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' -cp sonLib_daemonize.py ./bin/sonLib_daemonize.py -chmod +x ./bin/sonLib_daemonize.py -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' -. ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/reproducible-path/vg-1.59.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/reproducible-path/vg-1.59.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/reproducible-path/vg-1.59.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' -cd externalTools && make all -make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' -cd threeEdgeConnected && make all -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' -gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c [ 97%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 -ar rc 3EdgeConnected.a *.o -ranlib 3EdgeConnected.a -rm *.o -mv 3EdgeConnected.a ../..//../sonLib/lib/ -cp inc/*.h ../..//../sonLib/lib/ -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o +/usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wl,--dependency-file,CMakeFiles/vgio.dir/link.d -Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +[ 97%] 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/fast_locate.o src/fast_locate.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp [100%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' -make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' -gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I .//../sonLib/lib/ -c impl/*.c -gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a -/usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wl,--dependency-file,CMakeFiles/vgio.dir/link.d -Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -[100%] Built target vgio +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwt.o src/gbwt.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata.o src/metadata.cpp /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/ranlib libvgio.a make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' @@ -9741,9 +9750,15 @@ make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 0%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend -make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +[ 50%] Built target vgio +make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' @@ -9751,19 +9766,14 @@ make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -[ 50%] Built target vgio_static -[100%] Built target vgio +[100%] Built target vgio_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" @@ -9772,38 +9782,70 @@ -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/vg -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/vpkg.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_internal.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/fdstream.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_cppstream.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_input_stream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/loader.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_output_stream.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_emitter.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream_multiplexer.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_internal.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/loader.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_io.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/gafkluge.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/edit.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_cppstream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_iterator.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/basic_stream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_iterator.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/vpkg.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/json2pb.h --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_emitter.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/fdstream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/registry.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_emitter.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_emitter.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/gafkluge.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/edit.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_iterator.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/registry.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +. ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/reproducible-path/vg-1.59.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/reproducible-path/vg-1.59.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/reproducible-path/vg-1.59.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' +cd externalTools && make all +make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' +cd threeEdgeConnected && make all +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' +gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c +ar rc 3EdgeConnected.a *.o +ranlib 3EdgeConnected.a +rm *.o +mv 3EdgeConnected.a ../..//../sonLib/lib/ +cp inc/*.h ../..//../sonLib/lib/ +gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/test.o src/test.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' +make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' +gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -I inc -I .//../sonLib/lib/ -c impl/*.c +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/variants.o src/variants.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_gbwt.o src/build_gbwt.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_ri.o src/build_ri.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/merge_gbwt.o src/merge_gbwt.cpp ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ +gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/benchmark.o src/benchmark.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata_tool.o src/metadata_tool.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' +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 +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/gcsa2' +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' ar rcs lib/libgbwt.a obj/algorithms.o obj/bwtmerge.o obj/cached_gbwt.o obj/dynamic_gbwt.o obj/fast_locate.o obj/files.o obj/gbwt.o obj/internal.o obj/metadata.o obj/support.o obj/test.o obj/utils.o obj/variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_gbwt obj/build_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_ri obj/build_ri.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 @@ -9838,12 +9880,6 @@ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa2gbwt.o src/gfa2gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz_stats.o src/gbz_stats.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/kmer_freq.o src/kmer_freq.cpp -rm -f lib/libbdsg.a -ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/mapped_structs.o bdsg/obj/packed_graph.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/reference_path_overlay.o bdsg/obj/packed_reference_path_overlay.o bdsg/obj/path_subgraph_overlay.o bdsg/obj/subgraph_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/snarl_distance_index.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o -ar: creating lib/libbdsg.a -ar rcs lib/libgcsa2.a obj/algorithms.o obj/dbg.o obj/files.o obj/gcsa.o obj/internal.o obj/lcp.o obj/path_graph.o obj/support.o obj/utils.o -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a ar rcs lib/libgbwtgraph.a obj/algorithms.o obj/cached_gbwtgraph.o obj/gbwtgraph.o obj/gbz.o obj/gfa.o obj/internal.o obj/minimizer.o obj/path_cover.o obj/utils.o @@ -10157,8 +10193,6 @@ . ./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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp -. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp -. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:147:31: required from here @@ -10174,6 +10208,8 @@ /usr/include/google/protobuf/message_lite.h:381:7: note: declared here 381 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ +. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp +. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp @@ -10289,8 +10325,8 @@ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from -'/nonexistent/first-build/lib' and -'/nonexistent/first-build/include' +'/nonexistent/second-build/lib' and +'/nonexistent/second-build/include' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl @@ -11445,7 +11481,7 @@ # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' - make -j42 "INSTALL=install --strip-program=true" SFX=-ssse3 all test/build_graph bin/shuf + make -j20 "INSTALL=install --strip-program=true" SFX=-ssse3 all test/build_graph bin/shuf make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC @@ -11460,66 +11496,52 @@ . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/reproducible-path/vg-1.59.0+ds/include" make libs && cp lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/lib/ && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS && cp src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS/ . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp -r src/include/structures /build/reproducible-path/vg-1.59.0+ds/include/ rm -f lib/cleaned_old_protobuf* +rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' gcc -c -o ssw.o ssw.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -pipe -O3 -I. -g++ -c -o ssw_cpp.o ssw_cpp.cpp -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -pipe -O3 -I. -gcc -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' +g++ -c -o ssw_cpp.o ssw_cpp.cpp -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -pipe -O3 -I. Library will be installed in '/build/reproducible-path/vg-1.59.0+ds' -rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc +gcc -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c +gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c +rm -Rf include/google/protobuf deps/protobuf make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd externalTools && make all -gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' -if [ ! -d bin ]; then mkdir -p bin; fi +touch lib/cleaned_old_protobuf_v003 WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. -if [ ! -d obj ]; then mkdir -p obj; fi -rm -Rf include/google/protobuf deps/protobuf +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' +if [ ! -d bin ]; then mkdir -p bin; fi +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ rm -f /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/* +if [ ! -d obj ]; then mkdir -p obj; fi make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make all cd quicktree_1.1 && make all CC="gcc -std=c99" if [ ! -d lib ]; then mkdir -p lib; fi -touch lib/cleaned_old_protobuf_v003 -find bin obj lib -type f -delete make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' +find bin obj lib -type f -delete gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c -gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' +. ./source_me.sh && g++ -I -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/progress_bar.o deps/progress_bar/progress_bar.cpp gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' +gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c +gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c +gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj; fi -gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c if [ ! -d obj ]; then mkdir -p obj; fi -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o -gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c -. ./source_me.sh && g++ -I -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/progress_bar.o deps/progress_bar/progress_bar.cpp -g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp -gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -if [ ! -d lib ]; then mkdir -p lib; fi -gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test; fi -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/union_find.cpp -o obj/union_find.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin; fi -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o make[2]: 'bin/shuf' is up to date. -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib; fi -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps; fi -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. @@ -11529,15 +11551,12 @@ to work with policies introduced by or earlier. -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o +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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/union_find.cpp -o obj/union_find.o +if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib; fi +if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps; fi +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); @@ -11545,35 +11564,6 @@ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -./src/tree.c: In function ‘read_newhampshire_Tnode’: -./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 393 | fscanf( handle, "%1s", &c); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 406 | fscanf( handle, "%1s", &c); /* should be , */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 417 | fscanf( handle, "%1s", &c); /* should be ) */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 420 | fscanf( handle, "%1s", &c); /* should be : */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -./src/tree.c: In function ‘read_newhampshire_Tree’: -./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 468 | fscanf( handle, "("); - | ^~~~~~~~~~~~~~~~~~~~ -./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 475 | fscanf( handle, "%1s", &c ); /* should be , */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 484 | fscanf( handle, "%1s", &c ); /* should be , */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 493 | fscanf( handle, "%1s", &c); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 496 | fscanf( handle, "%1s", &c); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_graph_print’: src/gssw.c:1947:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1947 | fprintf(stdout, "GRAPH // node %llu %u %s\n", n->id, n->len, n->seq); @@ -11614,11 +11604,8 @@ | | | | long long unsigned int uint64_t {aka 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o src/gssw.c: In function ‘gssw_graph_print_score_matrices’: -/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: -/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] - 20 | } - | ^ src/gssw.c:1978:31: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1978 | fprintf(out, "node %llu\n", n->id); | ~~~^ ~~~~~ @@ -11650,87 +11637,170 @@ | | uint64_t {aka long unsigned int} | long long unsigned int | %lu -ar rc cuTest.a *.o +gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c +gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o +./src/tree.c: In function ‘read_newhampshire_Tnode’: +./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 393 | fscanf( handle, "%1s", &c); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 406 | fscanf( handle, "%1s", &c); /* should be , */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 417 | fscanf( handle, "%1s", &c); /* should be ) */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 420 | fscanf( handle, "%1s", &c); /* should be : */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +./src/tree.c: In function ‘read_newhampshire_Tree’: +./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 468 | fscanf( handle, "("); + | ^~~~~~~~~~~~~~~~~~~~ +./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 475 | fscanf( handle, "%1s", &c ); /* should be , */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 484 | fscanf( handle, "%1s", &c ); /* should be , */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 493 | fscanf( handle, "%1s", &c); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 496 | fscanf( handle, "%1s", &c); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o -- The C compiler identification is GNU 14.2.0 -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: -/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] - 96 | } - | ^ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o +ar rc cuTest.a *.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ +/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 | } + | ^ make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' --- The C compiler identification is GNU 14.2.0 --- Detecting CXX compiler ABI info +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o -- The CXX compiler identification is GNU 14.2.0 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o -- Detecting C compiler ABI info +gcc -o ssw_test ssw.o main.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -pipe -O3 -I. -lm -lz +gcc -o example_c ssw.o example.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -pipe -O3 -I. -lm -lz +g++ -o example_cpp example.cpp ssw.o ssw_cpp.o -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -pipe -O3 -I. -lm -lz -- The CXX compiler identification is GNU 14.2.0 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +-- The C compiler identification is GNU 14.2.0 +/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: +/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] + 96 | } + | ^ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o -- Detecting C compiler ABI info +-- Detecting CXX compiler ABI info +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)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Detecting C compiler ABI info - done --- Detecting C compiler ABI info - done -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' +-- Detecting CXX compiler ABI info +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 +ar: creating /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a +-- Detecting CXX compiler ABI info - done +-- Detecting C compiler ABI info - done +-- Check for working CXX compiler: /usr/bin/g++ - skipped +-- Detecting CXX compile features +-- Detecting CXX compile features - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done +gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' +-- Detecting CXX compiler ABI info 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' +-- Detecting C compiler ABI info cp inc/avl.h ../lib/avl.h.tmp cp inc/bioioC.h ../lib/bioioC.h.tmp cp inc/commonC.h ../lib/commonC.h.tmp cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp +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)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h -mv ../lib/commonC.h.tmp ../lib/commonC.h mv ../lib/bioioC.h.tmp ../lib/bioioC.h +mv ../lib/commonC.h.tmp ../lib/commonC.h mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h -mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp -cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp --- Detecting CXX compiler ABI info - done +mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h -mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h +cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp cp inc/jsmn.h ../lib/jsmn.h.tmp cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp cp inc/sonLib.h ../lib/sonLib.h.tmp cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp +cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp +mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h mv ../lib/jsmn.h.tmp ../lib/jsmn.h mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h +cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h -cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp -cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp -mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h -mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp -cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp -cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp +mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h +mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h -mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h -mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h +cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp +cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp -mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h -mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h +mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp +mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp +mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h +mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp -cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h +cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h -mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp +mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp @@ -11740,57 +11810,55 @@ mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h -mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp +mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp -mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h -mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp +mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/stGraph.h ../lib/stGraph.h.tmp +mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/stJson.h ../lib/stJson.h.tmp -cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h +cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h mv ../lib/stJson.h.tmp ../lib/stJson.h mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp --- Check for working CXX compiler: /usr/bin/g++ - skipped --- Detecting CXX compile features -mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h -mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp --- Detecting CXX compile features - done cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp -cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp -cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp +mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h +mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h +cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp +cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C --- Detecting C compiler ABI info --- Detecting CXX compiler ABI info --- Detecting CXX compiler ABI info -gcc -o ssw_test ssw.o main.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -pipe -O3 -I. -lm -lz -gcc -o example_c ssw.o example.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -pipe -O3 -I. -lm -lz -g++ -o example_cpp example.cpp ssw.o ssw_cpp.o -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -pipe -O3 -I. -lm -lz -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -rm -f lib/libstructures.a -ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o -ar: creating lib/libstructures.a -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' -src/gssw.c: In function ‘gssw_sw_software_byte’: -src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] - 277 | memcpy(scratch, to_unswizzle, size); - | ^ -In function ‘unswizzle_byte’, - inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: -src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ - 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +-- Detecting CXX compiler ABI info - done +-- Check for working CXX compiler: /usr/bin/g++ - skipped +-- Detecting CXX compile features +-- Detecting CXX compile features - done +-- Configuring done (5.2s) +-- Generating done (0.0s) +-- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +[ 16%] Building CXX object CMakeFiles/kff.dir/kff_io.cpp.o +-- Detecting CXX compiler ABI info - done +-- Detecting C compiler ABI info - done +-- Check for working CXX compiler: /usr/bin/g++ - skipped +-- Detecting CXX compile features +-- Detecting CXX compile features - done cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +-- Check for working C compiler: /usr/bin/gcc - skipped +-- Detecting C compile features +-- Detecting C compile features - done 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)) { @@ -11812,129 +11880,90 @@ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ --- Detecting C compiler ABI info - done --- Detecting CXX compiler ABI info - done --- Detecting CXX compiler ABI info - done --- Check for working CXX compiler: /usr/bin/g++ - skipped --- Detecting CXX compile features --- Check for working C compiler: /usr/bin/gcc - skipped --- Detecting C compile features --- Detecting CXX compile features - done --- Detecting C compile features - done -libhandlegraph is root project or external_project +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); + | ^~~~~~~~~~~ -- Compiler is recent enough to support C++14. --- Configuring done (1.9s) --- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG --- Check for working CXX compiler: /usr/bin/g++ - skipped --- Detecting CXX compile features --- Detecting CXX compile features - done --- Configuring done (1.9s) --- Generating done (0.0s) +libhandlegraph is root project or external_project-- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG + +-- Configuring done (5.8s) +-- Generating done (0.2s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 --- Generating done (0.0s) --- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make 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-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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/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 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CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/extend.cpp -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/chop.cpp -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 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for C++/ObjC++ but not for C --- Performing Test HAVE_CXA_DEMANGLE -src/gssw.c: In function ‘gssw_sw_software_word’: -src/gssw.c:1117:5: warning: ‘__builtin_memcpy’ writing between 18446744069414584336 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] - 1117 | memcpy(scratch, to_unswizzle, size * sizeof(int16_t)); - | ^ -In function ‘unswizzle_word’, - inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: -src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ - 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 68%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -- Performing Test HAVE_CXA_DEMANGLE - Success +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. 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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 +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c 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Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -src/gssw.c: In function ‘gssw_node_create’: -src/gssw.c:4975:5: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - 4975 | strncpy(n->seq, seq, len); n->seq[len] = 0; - | ^ -src/gssw.c:4971:19: note: length computed here - 4971 | int32_t len = strlen(seq); - | ^~~~~~~~~~~ --- Configuring done (3.7s) +[ 85%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o +[ 88%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time 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+/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/extend.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +ar rc /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o 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/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 --- Generating done (0.4s) +ranlib /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a +-- Generating done (0.9s) -- 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[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' 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 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lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -[ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -[ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o -[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o +[ 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 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lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp -[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o -[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra 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lib/CMakeFiles/sdsl.dir/config.cpp.o +[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp +[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o +cd 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lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp +[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o +[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp -[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd 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CMakeFiles/sdsl.dir/simple_sds.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/simple_sds.cpp -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/structure_tree.cpp -[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o -[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint128_t.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/wt_helper.cpp -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/vector:63, - from /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:8: -In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = long int]’, - inlined from ‘static void std::allocator_traits >::deallocate(allocator_type&, pointer, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:544:23, - inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:389:19, - inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:368:15, - inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:738:7, - inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:445:5: -/usr/include/c++/14/bits/new_allocator.h:172:33: warning: ‘void operator delete(void*, std::size_t)’ called on pointer ‘’ with nonzero offset [1, 9223372036854775800] [-Wfree-nonheap-object] - 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); - | ^ -In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = long int]’, - inlined from ‘static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:509:28, - inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:380:33, - inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:398:44, - inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:334:26, - inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const value_type&, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:571:47, - inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:327:85: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from ‘void* operator new(std::size_t)’ - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa.cpp 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); @@ -12080,10 +12060,15 @@ /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp +[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -ar rc /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o -ranlib /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/io.cpp +# Make dest directory +gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz impl/sonLibConnectivity.c: In function ‘stConnectivity_addEdge’: impl/sonLibConnectivity.c:248:33: warning: pointer ‘component1’ may be used after ‘free’ [-Wuse-after-free] 248 | connectivity->mergeCallback(connectivity->mergeExtraData, component1, component2); @@ -12093,23 +12078,67 @@ impl/sonLibConnectivity.c:608:9: note: call to ‘free’ here 608 | free(comp); | ^~~~~~~~~~ +gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/vector:63, + from /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:8: +In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = long int]’, + inlined from ‘static void std::allocator_traits >::deallocate(allocator_type&, pointer, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:544:23, + inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:389:19, + inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:368:15, + inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:738:7, + inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:445:5: +/usr/include/c++/14/bits/new_allocator.h:172:33: warning: ‘void operator delete(void*, std::size_t)’ called on pointer ‘’ with nonzero offset [1, 9223372036854775800] [-Wfree-nonheap-object] + 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); + | ^ +In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = long int]’, + inlined from ‘static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:509:28, + inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:380:33, + inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:398:44, + inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:334:26, + inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const value_type&, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:571:47, + inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:327:85: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from ‘void* operator new(std::size_t)’ + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 33%] Linking CXX static library libkff.a +gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 33%] Built target kff +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/louds_tree.cpp +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/memory_management.cpp 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 +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +ar rvs lib/libgssw.a obj/gssw.o +ar: creating lib/libgssw.a +a - obj/gssw.o +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp +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' -[ 66%] Building CXX object CMakeFiles/kff_example.dir/main.cpp.o +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp [ 66%] Building CXX object benchmarks/CMakeFiles/reader_bench.dir/reader.cpp.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_fs.cpp +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: @@ -12122,30 +12151,37 @@ /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:448:9: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 448 | *word &= | ^~~~~ -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -# Make dest directory -gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz -gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz -gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz -ar rvs lib/libgssw.a obj/gssw.o -ar: creating lib/libgssw.a -a - obj/gssw.o -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 83%] Linking CXX executable reader_bench -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/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 +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 83%] Built target reader_bench cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sfstream.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o -MF CMakeFiles/sdsl.dir/simple_sds.cpp.o.d -o CMakeFiles/sdsl.dir/simple_sds.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/simple_sds.cpp +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/structure_tree.cpp [100%] Linking CXX executable kff_example -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint128_t.cpp +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [100%] Built target kff_example make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/wt_helper.cpp +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C @@ -12158,10 +12194,6 @@ | ^~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 94%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend @@ -12171,23 +12203,26 @@ make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 97%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 [100%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +/usr/bin/g++ -fPIC -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,--dependency-file,CMakeFiles/handlegraph_shared.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +[100%] Built target handlegraph_shared +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -/usr/bin/g++ -fPIC -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,--dependency-file,CMakeFiles/handlegraph_shared.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Built target handlegraph_static -[100%] Built target handlegraph_shared make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' @@ -12199,6 +12234,7 @@ make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' @@ -12213,19 +12249,18 @@ cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +[ 97%] Built target handlegraph_static [100%] Built target handlegraph_shared -[100%] Built target handlegraph_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[4]: Nothing to be done for 'preinstall'. @@ -12236,48 +12271,48 @@ -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.a -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_deletable_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_metadata.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_metadata.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_position_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/deletable_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/util.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/buildable_snarl_decomposition.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/trivially_serializable.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/iteratee.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_handle_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_metadata.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/types.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/snarl_decomposition.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/named_node_back_translation.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_metadata.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_tips.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/count_walks.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/split_strands.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/eades_algorithm.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/are_equivalent.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dijkstra.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/append_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/apply_orientations.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal/dfs.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dagify.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/reverse_complement.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_shortest_paths.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/topological_sort.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/copy_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/strongly_connected_components.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/chop.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/extend.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/weakly_connected_components.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_single_stranded.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/chop.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_shortest_paths.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/are_equivalent.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_acyclic.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/snarl_decomposition.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/types.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/named_node_back_translation.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dijkstra.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/append_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/apply_orientations.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_single_stranded.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/count_walks.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/weakly_connected_components.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/eades_algorithm.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/topological_sort.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/copy_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_tips.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dagify.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/expanding_overlay_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/trivially_serializable.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/iteratee.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_handle_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_mutable_handle_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_position_handle_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphConfig.cmake @@ -12286,63 +12321,55 @@ rm -f /build/reproducible-path/vg-1.59.0+ds/include/vg.pb.h /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp" && export LDFLAGS="-Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && rm -rf build-vg && mkdir build-vg && cd build-vg && PKG_CONFIG_PATH=/build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig: cmake -DCMAKE_CXX_STANDARD=14 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH="/usr;/" -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make clean && VERBOSE=1 make && make install -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp -ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o -ranlib sonLib.a -rm *.o -mv sonLib.a ../lib/ -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm -mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest -mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") Building libvgio for C++ 14 -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Could NOT find Protobuf (missing: Protobuf_DIR) No installed Protobuf has registered itself with CMake. +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.21.12") Found Protobuf using FindProtobuf.cmake -- Found Threads: TRUE Using real Threads library -- Checking for module 'htslib' -- Found htslib, version 1.20 +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Checking for module 'jansson' -- Found jansson, version 2.14 Using installed libhandlegraph --- Configuring done (0.9s) +-- Configuring done (3.4s) +g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg +ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +/usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make -f CMakeFiles/test_libvgio.dir/build.make CMakeFiles/test_libvgio.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -/usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake +/usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +/usr/bin/cmake -P CMakeFiles/test_libvgio.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -/usr/bin/cmake -P CMakeFiles/test_libvgio.dir/cmake_clean.cmake -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -/usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake -mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +ranlib sonLib.a make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' @@ -12365,86 +12392,91 @@ make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 2%] Running cpp protocol buffer compiler on deps/vg.proto -[ 5%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto +[ 5%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto +rm *.o +mv sonLib.a ../lib/ +gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm +gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 +gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm +gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +[ 8%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o [ 11%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -[ 11%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -[ 14%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o -[ 17%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -[ 20%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_emitter.cpp -[ 26%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -[ 23%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o -[ 29%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o -[ 32%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o -/usr/bin/g++ 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CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/registry.cpp.o -MF CMakeFiles/vgio.dir/src/registry.cpp.o.d -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/registry.cpp -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg 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-Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/vpkg.cpp -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 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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 +[ 67%] 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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 +[ 70%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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 +[ 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream_multiplexer.cpp +[ 76%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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 +[ 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 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82%] 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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 +[ 85%] 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/simple_sds.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 +[ 88%] Building CXX 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -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 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Removing old files @@ -12456,8 +12488,12 @@ make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend +[ 94%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o +[ 94%] 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 -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream_multiplexer.cpp make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio_static.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/vpkg.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' @@ -12601,114 +12637,77 @@ rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' mkdir -p bin mkdir -p lib -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' mkdir -p obj -[ ! -e bdsg/obj ] || rm -r bdsg/obj -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' rm -rf bin lib obj -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' rm -f *.o *.a build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' cd tests && make clean +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dbg.o src/dbg.cpp +[ ! -e bdsg/obj ] || rm -r bdsg/obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gcsa.o src/gcsa.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/lcp.o src/lcp.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_graph.o src/path_graph.cpp rm -f test_bwtmerge test_metadata test_queries test_support test_variants *.o -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' -[ ! -e lib ] || rm -r lib mkdir -p bin +[ ! -e lib ] || rm -r lib mkdir -p lib mkdir -p obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp +[ ! -e bin ] || rm -r bin +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/bwtmerge.o src/bwtmerge.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwt.o src/cached_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dynamic_gbwt.o src/dynamic_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/fast_locate.o src/fast_locate.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwt.o src/gbwt.cpp -[ ! -e bin ] || rm -r bin -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/mapped_structs.cpp -o bdsg/obj/mapped_structs.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/reference_path_overlay.cpp -o bdsg/obj/reference_path_overlay.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_reference_path_overlay.cpp -o bdsg/obj/packed_reference_path_overlay.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/path_subgraph_overlay.cpp -o bdsg/obj/path_subgraph_overlay.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/subgraph_overlay.cpp -o bdsg/obj/subgraph_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata.o src/metadata.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/mapped_structs.cpp -o bdsg/obj/mapped_structs.o +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' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/test.o src/test.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/variants.o src/variants.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_gbwt.o src/build_gbwt.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/lcp.o src/lcp.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_graph.o src/path_graph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_ri.o src/build_ri.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/merge_gbwt.o src/merge_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/benchmark.o src/benchmark.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata_tool.o src/metadata_tool.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o -mv ../bin/sonLibTests.tmp ../bin/sonLibTests -make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' -cp sonLib_daemonize.py ./bin/sonLib_daemonize.py -chmod +x ./bin/sonLib_daemonize.py -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' -. ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/reproducible-path/vg-1.59.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/reproducible-path/vg-1.59.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/reproducible-path/vg-1.59.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' -cd externalTools && make all -make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' -cd threeEdgeConnected && make all -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' -gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c -ar rc 3EdgeConnected.a *.o -ranlib 3EdgeConnected.a -rm *.o -mv 3EdgeConnected.a ../..//../sonLib/lib/ -cp inc/*.h ../..//../sonLib/lib/ -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' -make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' -gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I .//../sonLib/lib/ -c impl/*.c -gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a -ar rc stPinchesAndCacti.a *.o -ranlib stPinchesAndCacti.a -rm *.o -mv stPinchesAndCacti.a .//../sonLib/lib/ -cp inc/*.h .//../sonLib/lib/ -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' -[ 97%] Linking CXX shared library libvgio.so -/usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 -[100%] Linking CXX static library libvgio.a +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp +[ 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 +[100%] Linking CXX shared library libvgio.so +/usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wl,--dependency-file,CMakeFiles/vgio.dir/link.d -Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -/usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 -[100%] Built target vgio /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/ranlib libvgio.a make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +[100%] Built target vgio [100%] Built target vgio_static +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata_tool.o src/metadata_tool.cpp make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' @@ -12727,23 +12726,24 @@ make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 0%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend -make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" +make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o +[ 50%] Built target vgio +make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [100%] Built target vgio_static -[100%] Built target vgio make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall @@ -12755,35 +12755,71 @@ -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libvgio.so -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libvgio.a +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/vg -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/vpkg.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_internal.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_input_stream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/loader.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_output_stream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream_multiplexer.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_io.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_cppstream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/basic_stream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_iterator.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/json2pb.h --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_emitter.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/fdstream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/registry.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_emitter.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_emitter.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_iterator.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream_multiplexer.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_internal.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/loader.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/edit.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_emitter.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/vpkg.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_output_stream.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/json2pb.h +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_emitter.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_iterator.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/registry.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +. ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/reproducible-path/vg-1.59.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/reproducible-path/vg-1.59.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/reproducible-path/vg-1.59.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' +cd externalTools && make all +make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' +cd threeEdgeConnected && make all +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' +gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c +ar rc 3EdgeConnected.a *.o +ranlib 3EdgeConnected.a +rm *.o +mv 3EdgeConnected.a ../..//../sonLib/lib/ +cp inc/*.h ../..//../sonLib/lib/ +gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' +make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' +gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -I inc -I .//../sonLib/lib/ -c impl/*.c +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/reference_path_overlay.cpp -o bdsg/obj/reference_path_overlay.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_reference_path_overlay.cpp -o bdsg/obj/packed_reference_path_overlay.o +gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/path_subgraph_overlay.cpp -o bdsg/obj/path_subgraph_overlay.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/subgraph_overlay.cpp -o bdsg/obj/subgraph_overlay.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o +ar rc stPinchesAndCacti.a *.o +ranlib stPinchesAndCacti.a +rm *.o +mv stPinchesAndCacti.a .//../sonLib/lib/ +cp inc/*.h .//../sonLib/lib/ +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' ar rcs lib/libgbwt.a obj/algorithms.o obj/bwtmerge.o obj/cached_gbwt.o obj/dynamic_gbwt.o obj/fast_locate.o obj/files.o obj/gbwt.o obj/internal.o obj/metadata.o obj/support.o obj/test.o obj/utils.o obj/variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_gbwt obj/build_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_ri obj/build_ri.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 @@ -12818,12 +12854,12 @@ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa2gbwt.o src/gfa2gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz_stats.o src/gbz_stats.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/kmer_freq.o src/kmer_freq.cpp +ar rcs lib/libgcsa2.a obj/algorithms.o obj/dbg.o obj/files.o obj/gcsa.o obj/internal.o obj/lcp.o obj/path_graph.o obj/support.o obj/utils.o +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/mapped_structs.o bdsg/obj/packed_graph.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/reference_path_overlay.o bdsg/obj/packed_reference_path_overlay.o bdsg/obj/path_subgraph_overlay.o bdsg/obj/subgraph_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/snarl_distance_index.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' -ar rcs lib/libgcsa2.a obj/algorithms.o obj/dbg.o obj/files.o obj/gcsa.o obj/internal.o obj/lcp.o obj/path_graph.o obj/support.o obj/utils.o -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a ar rcs lib/libgbwtgraph.a obj/algorithms.o obj/cached_gbwtgraph.o obj/gbwtgraph.o obj/gbz.o obj/gfa.o obj/internal.o obj/minimizer.o obj/path_cover.o obj/utils.o @@ -13135,7 +13171,6 @@ . ./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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/haplotypes_main.o src/subcommand/haplotypes_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp -. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:147:31: required from here @@ -13151,6 +13186,7 @@ /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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp @@ -13269,8 +13305,8 @@ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/progress_bar' cd ./deps && cd sdsl-lite && ./uninstall.sh || true Library files will be removed from -'/nonexistent/first-build/lib' and -'/nonexistent/first-build/include' +'/nonexistent/second-build/lib' and +'/nonexistent/second-build/include' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 uninstall-sdsl @@ -14425,7 +14461,7 @@ # lru_cache is never built because it is header-only # bash-tap is never built either make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' - make -j42 "INSTALL=install --strip-program=true" SFX=-sse3 all test/build_graph bin/shuf + make -j20 "INSTALL=install --strip-program=true" SFX=-sse3 all test/build_graph bin/shuf make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC @@ -14438,73 +14474,53 @@ . ./source_me.sh && cd deps/gssw && make && cp lib/libgssw.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp src/gssw.h /build/reproducible-path/vg-1.59.0+ds/include/ . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/reproducible-path/vg-1.59.0+ds/include" make libs && cp lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/lib/ && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS && cp src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS/ -. ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp -r src/include/structures /build/reproducible-path/vg-1.59.0+ds/include/ -rm -f lib/cleaned_old_protobuf* +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/ssw/src' gcc -c -o ssw.o ssw.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -pipe -O3 -I. +. ./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/ g++ -c -o ssw_cpp.o ssw_cpp.cpp -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -pipe -O3 -I. +rm -f lib/cleaned_old_protobuf* gcc -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' -Library will be installed in '/build/reproducible-path/vg-1.59.0+ds' -gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +WARNING: .git/hooks directory does not exists. + The pre-commit hook is not installed. rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc +rm -Rf include/google/protobuf deps/protobuf 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/gssw' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd externalTools && make all -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +touch lib/cleaned_old_protobuf_v003 make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi rm -f /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/* -WARNING: .git/hooks directory does not exists. - The pre-commit hook is not installed. +gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c if [ ! -d obj ]; then mkdir -p obj; fi -rm -Rf include/google/protobuf deps/protobuf make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make all -if [ ! -d lib ]; then mkdir -p lib; fi cd quicktree_1.1 && make all CC="gcc -std=c99" make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' -touch lib/cleaned_old_protobuf_v003 +if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' +. ./source_me.sh && g++ -I -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/progress_bar.o deps/progress_bar/progress_bar.cpp +g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' +gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c -gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c -gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj; fi -gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c +gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o +make[2]: 'bin/shuf' is up to date. +gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o if [ ! -d obj ]; then mkdir -p obj; fi -gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c -gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test; fi -if [ ! -d lib ]; then mkdir -p lib; fi -. ./source_me.sh && g++ -I -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/progress_bar.o deps/progress_bar/progress_bar.cpp -g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin; fi -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/union_find.cpp -o obj/union_find.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib; fi -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o -make[2]: 'bin/shuf' is up to date. -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o -if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps; fi -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. @@ -14514,10 +14530,14 @@ to work with policies introduced by or earlier. -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o +if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test; fi +if [ ! -d /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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/union_find.cpp -o obj/union_find.o +if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib; fi +if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps; fi +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); @@ -14525,42 +14545,9 @@ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -./src/tree.c: In function ‘read_newhampshire_Tnode’: -./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 393 | fscanf( handle, "%1s", &c); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 406 | fscanf( handle, "%1s", &c); /* should be , */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 417 | fscanf( handle, "%1s", &c); /* should be ) */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 420 | fscanf( handle, "%1s", &c); /* should be : */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -./src/tree.c: In function ‘read_newhampshire_Tree’: -./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 468 | fscanf( handle, "("); - | ^~~~~~~~~~~~~~~~~~~~ -./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 475 | fscanf( handle, "%1s", &c ); /* should be , */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 484 | fscanf( handle, "%1s", &c ); /* should be , */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 493 | fscanf( handle, "%1s", &c); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 496 | fscanf( handle, "%1s", &c); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ --- The C compiler identification is GNU 14.2.0 --- The C compiler identification is GNU 14.2.0 --- The CXX compiler identification is GNU 14.2.0 -/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: -/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] - 20 | } - | ^ +gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c +gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c +gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c src/gssw.c: In function ‘gssw_graph_print’: src/gssw.c:1947:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1947 | fprintf(stdout, "GRAPH // node %llu %u %s\n", n->id, n->len, n->seq); @@ -14609,9 +14596,7 @@ | | uint64_t {aka long unsigned int} | long long unsigned int | %lu --- The CXX compiler identification is GNU 14.2.0 src/gssw.c: In function ‘gssw_print_graph_cigar’: --- Detecting C compiler ABI info src/gssw.c:3623:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 3623 | fprintf(out, "%llu[", nc->node->id); | ~~~^ ~~~~~~~~~~~~ @@ -14619,8 +14604,38 @@ | | uint64_t {aka long unsigned int} | long long unsigned int | %lu --- The CXX compiler identification is GNU 14.2.0 +-- 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o src/gssw.c: In function ‘gssw_create_seed_byte’: +./src/tree.c: In function ‘read_newhampshire_Tnode’: +./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 393 | fscanf( handle, "%1s", &c); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 406 | fscanf( handle, "%1s", &c); /* should be , */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 417 | fscanf( handle, "%1s", &c); /* should be ) */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 420 | fscanf( handle, "%1s", &c); /* should be : */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +./src/tree.c: In function ‘read_newhampshire_Tree’: +./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 468 | fscanf( handle, "("); + | ^~~~~~~~~~~~~~~~~~~~ +./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 475 | fscanf( handle, "%1s", &c ); /* should be , */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 484 | fscanf( handle, "%1s", &c ); /* should be , */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 493 | fscanf( handle, "%1s", &c); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 496 | fscanf( handle, "%1s", &c); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: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); | ~~~^ ~~~~~~~~~~~ @@ -14629,7 +14644,6 @@ | long long unsigned int | %lu src/gssw.c: In function ‘gssw_create_seed_word’: --- Detecting C compiler ABI info src/gssw.c:5130:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5130 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); | ~~~^ ~~~~~~~~~~~ @@ -14637,249 +14651,264 @@ | | uint64_t {aka long unsigned int} | long long unsigned int | %lu +-- The CXX compiler identification is GNU 14.2.0 -- The C compiler identification is GNU 14.2.0 --- Detecting CXX compiler ABI info --- Detecting C compiler ABI info - done +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o +-- The CXX compiler identification is GNU 14.2.0 ar rc cuTest.a *.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o ranlib cuTest.a --- Check for working C compiler: /usr/bin/gcc - skipped --- Detecting C compile features --- Detecting C compile features - done +-- Detecting C compiler ABI info rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ +-- The C compiler identification is GNU 14.2.0 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o +-- Detecting CXX compiler ABI info +-- The CXX compiler identification is GNU 14.2.0 +-- Detecting C compiler ABI info +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o +/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 | } + | ^ +-- 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 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o -- Detecting CXX compiler ABI info --- Detecting CXX compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done +-- Detecting CXX compiler ABI info - done +-- Detecting CXX compiler ABI info +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done --- Detecting CXX compiler ABI info -- Detecting C compiler ABI info -/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: -/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] - 96 | } - | ^ --- Detecting CXX compiler ABI info - done --- Detecting C compiler ABI info - done -- Detecting CXX compiler ABI info - done +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done +-- Detecting CXX compiler ABI info - done libhandlegraph is root project or external_project --- Check for working C compiler: /usr/bin/gcc - skipped --- Detecting C compile features --- Configuring done (0.7s) --- Detecting C compile features - done --- Compiler is recent enough to support C++14. --- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG +-- Configuring done (2.3s) -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done --- Generating done (0.0s) +-- Generating done (0.1s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --- Configuring done (0.7s) -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -/usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 +-- Configuring done (2.4s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +/usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 +-- Detecting C compiler ABI info - done make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 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Success +/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 | } + | ^ +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/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' -[ 85%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o cd C && make all -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. 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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/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp +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 mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp -cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h +cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h +g++ -o example_cpp example.cpp ssw.o ssw_cpp.o -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -pipe -O3 -I. -lm -lz cp inc/sonLib.h ../lib/sonLib.h.tmp -cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' mv ../lib/sonLib.h.tmp ../lib/sonLib.h +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h +[ 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_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/sonLibCache.h ../lib/sonLibCache.h.tmp -cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h +cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp +[ 20%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_metadata.cpp +[ 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_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/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp -cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h -mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h +[ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o +-- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG - Success +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp +-- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS +cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp -cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp +mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h -mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h +cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp +mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h +[ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/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 mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp -cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h +src/gssw.c: In function ‘gssw_sw_software_byte’: +src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] + 277 | memcpy(scratch, to_unswizzle, size); + | ^ +In function ‘unswizzle_byte’, + inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: +src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ + 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h -[ 91%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp -cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h +[ 28%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h -[ 94%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o +cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp +[ 34%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o +[ 34%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/serializable.cpp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/extend.cpp +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/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 cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp -cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp -cp inc/sonLibString.h ../lib/sonLibString.h.tmp +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/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 mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h --- Performing Test HAVE_CXA_DEMANGLE +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 -cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp +[ 40%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h -cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/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 +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 -cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h +cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp -cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h +cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp -cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h -cp inc/stSafeC.h ../lib/stSafeC.h.tmp +cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h +cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp -cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h +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 -o ssw_test ssw.o main.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -pipe -O3 -I. -lm -lz gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -I inc -I ../lib/ -c impl/*.c -gcc -o example_c ssw.o example.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -pipe -O3 -I. -lm -lz -rm -f lib/libstructures.a -ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o -ar: creating lib/libstructures.a +-- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' -g++ -o example_cpp example.cpp ssw.o ssw_cpp.o -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -pipe -O3 -I. -lm -lz -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ --- Performing Test HAVE_CXA_DEMANGLE - Success --- Compiler supports DEMANGLE. --- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE --- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success --- Could NOT find Git (missing: GIT_EXECUTABLE) -CMake Warning at CMakeLists.txt:102 (message): - git not found. Cloning of submodules will not work. - - --- Looking for C++ include cstdio --- Looking for C++ include cstdio - found +[ 42%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/append_graph.cpp +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 +[ 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/are_equivalent.cpp +[ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o +-- Performing Test HAVE_CXA_DEMANGLE +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_tips.cpp +[ 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/topological_sort.cpp +[ 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/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 +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)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 60%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp +[ 62%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/count_walks.cpp +[ 65%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 +[ 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp +[ 71%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp 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] @@ -14902,28 +14931,52 @@ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ --- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -src/gssw.c: In function ‘gssw_sw_software_byte’: -src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] - 277 | memcpy(scratch, to_unswizzle, size); +[ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp +[ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dijkstra.cpp +-- Performing Test HAVE_CXA_DEMANGLE - Success +-- Compiler supports DEMANGLE. +-- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE +src/gssw.c: In function ‘gssw_node_create’: +src/gssw.c:4975:5: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] + 4975 | strncpy(n->seq, seq, len); n->seq[len] = 0; | ^ -In function ‘unswizzle_byte’, - inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: -src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ - 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --- Configuring done (2.6s) -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' -ar: creating /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a --- Generating done (0.2s) +src/gssw.c:4971:19: note: length computed here + 4971 | int32_t len = strlen(seq); + | ^~~~~~~~~~~ +[ 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 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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 +-- 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 +[ 88%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o +[ 91%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/chop.cpp +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 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-fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/extend.cpp +-- Looking for C++ include cstdio - found +-- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot +-- Configuring done (9.3s) +-- Generating done (1.1s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 8 -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend @@ -14932,73 +14985,35 @@ make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' -[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF 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/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include 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-I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp +[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o +[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/config.cpp +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 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CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_isa.cpp -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o +[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o +[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa.cpp -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o +[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp +[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp +cc1: warning: command-line option 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/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 +[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG 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-I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/louds_tree.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g 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-I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sd_vector.cpp -[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o -[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. 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lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o -MF CMakeFiles/sdsl.dir/simple_sds.cpp.o.d -o CMakeFiles/sdsl.dir/simple_sds.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/simple_sds.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/structure_tree.cpp -[ 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-I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/wt_helper.cpp -src/gssw.c: In function ‘gssw_sw_software_word’: -src/gssw.c:1117:5: warning: ‘__builtin_memcpy’ writing between 18446744069414584336 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] - 1117 | memcpy(scratch, to_unswizzle, size * sizeof(int16_t)); - | ^ -In function ‘unswizzle_word’, - inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: -src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ - 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/vector:63, @@ -15022,44 +15037,29 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from ‘void* operator new(std::size_t)’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -src/gssw.c: In function ‘gssw_node_create’: -src/gssw.c:4975:5: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] - 4975 | strncpy(n->seq, seq, len); n->seq[len] = 0; - | ^ -src/gssw.c:4971:19: note: length computed here - 4971 | int32_t len = strlen(seq); - | ^~~~~~~~~~~ -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +ranlib /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/io.cpp +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/louds_tree.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 33%] Linking CXX static library libkff.a -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 33%] Built target kff make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -In file included from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, - from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, - from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: -In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, - inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, - inlined from ‘void sdsl::int_vector< >::bit_resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1358:27, - inlined from ‘void sdsl::int_vector< >::resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:380:23, - inlined from ‘sdsl::int_vector< >::int_vector(size_type, value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1285:11, - inlined from ‘sdsl::excess::impl::impl()’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: -/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:448:9: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] - 448 | *word &= - | ^~~~~ -[ 66%] Building CXX object benchmarks/CMakeFiles/reader_bench.dir/reader.cpp.o -[ 66%] Building CXX object CMakeFiles/kff_example.dir/main.cpp.o +[ 50%] Building CXX object CMakeFiles/kff_example.dir/main.cpp.o +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +# Make dest directory +gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/example.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 +gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] @@ -15084,9 +15084,23 @@ 774 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -ar rc /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o -[ 83%] Linking CXX executable reader_bench -ranlib /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a +gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/memory_management.cpp +ar rvs lib/libgssw.a obj/gssw.o +ar: creating lib/libgssw.a +a - obj/gssw.o +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/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 +[ 66%] Building CXX object benchmarks/CMakeFiles/reader_bench.dir/reader.cpp.o +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_fs.cpp +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' 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); @@ -15096,51 +15110,61 @@ impl/sonLibConnectivity.c:608:9: note: call to ‘free’ here 608 | free(comp); | ^~~~~~~~~~ +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -[ 83%] Built target reader_bench -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -# Make dest directory -gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz -gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz -gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz -ar rvs lib/libgssw.a obj/gssw.o -ar: creating lib/libgssw.a -a - obj/gssw.o +[ 83%] Linking CXX executable reader_bench [100%] Linking CXX executable kff_example +In file included from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, + from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, + from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: +In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, + inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, + inlined from ‘void sdsl::int_vector< >::bit_resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1358:27, + inlined from ‘void sdsl::int_vector< >::resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:380:23, + inlined from ‘sdsl::int_vector< >::int_vector(size_type, value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1285:11, + inlined from ‘sdsl::excess::impl::impl()’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: +/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:448:9: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] + 448 | *word &= + | ^~~~~ +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sfstream.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [100%] Built target kff_example +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/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 +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[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/structure_tree.cpp +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint128_t.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/wt_helper.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -impl/sonLibTreap.c: In function ‘stTreap_remove’: -impl/sonLibTreap.c:331:18: warning: pointer ‘rmnode’ used after ‘free’ [-Wuse-after-free] - 331 | stTreap *p = rmnode->parent; - | ^ -impl/sonLibTreap.c:329:9: note: call to ‘free’ here - 329 | free(rmnode); - | ^~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 94%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend @@ -15149,24 +15173,30 @@ make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +make[5]: 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' -[100%] Linking CXX static library libhandlegraph.a [100%] Linking CXX shared library libhandlegraph.so +[100%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +impl/sonLibTreap.c: In function ‘stTreap_remove’: +impl/sonLibTreap.c:331:18: warning: pointer ‘rmnode’ used after ‘free’ [-Wuse-after-free] + 331 | stTreap *p = rmnode->parent; + | ^ +impl/sonLibTreap.c:329:9: note: call to ‘free’ here + 329 | free(rmnode); + | ^~~~~~~~~~~~ /usr/bin/g++ -fPIC -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,--dependency-file,CMakeFiles/handlegraph_shared.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Built target handlegraph_shared /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [100%] Built target handlegraph_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 @@ -15191,18 +15221,19 @@ cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -make[5]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. +make[5]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +[ 97%] Built target handlegraph_static +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' +make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -make[5]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. +make[5]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' -[ 97%] Built target handlegraph_shared -[100%] Built target handlegraph_static +[100%] Built target handlegraph_shared make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall @@ -15215,48 +15246,48 @@ -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.a -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_deletable_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_metadata.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_metadata.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_position_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/deletable_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/expanding_overlay_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/util.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/buildable_snarl_decomposition.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/trivially_serializable.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/iteratee.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_handle_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_metadata.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/types.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/snarl_decomposition.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/named_node_back_translation.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_metadata.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_tips.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/count_walks.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/split_strands.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/eades_algorithm.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/are_equivalent.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dijkstra.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/append_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/apply_orientations.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal/dfs.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dagify.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/reverse_complement.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_shortest_paths.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/topological_sort.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/copy_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/strongly_connected_components.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/chop.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/extend.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/weakly_connected_components.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_single_stranded.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/chop.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_shortest_paths.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/are_equivalent.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_acyclic.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/snarl_decomposition.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/types.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/named_node_back_translation.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dijkstra.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/append_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/apply_orientations.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_single_stranded.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/count_walks.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/weakly_connected_components.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/eades_algorithm.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/topological_sort.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/copy_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_tips.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dagify.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/expanding_overlay_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/trivially_serializable.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/iteratee.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_handle_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/deletable_handle_graph.hpp -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable_handle_graph.hpp --- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_mutable_handle_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_position_handle_graph.hpp +-- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphConfig.cmake @@ -15265,18 +15296,23 @@ rm -f /build/reproducible-path/vg-1.59.0+ds/include/vg.pb.h /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp" && export LDFLAGS="-Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && rm -rf build-vg && mkdir build-vg && cd build-vg && PKG_CONFIG_PATH=/build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig: cmake -DCMAKE_CXX_STANDARD=14 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH="/usr;/" -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make clean && VERBOSE=1 make && make install +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") Building libvgio for C++ 14 -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Could NOT find Protobuf (missing: Protobuf_DIR) No installed Protobuf has registered itself with CMake. +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.21.12") Found Protobuf using FindProtobuf.cmake -- Found Threads: TRUE @@ -15285,29 +15321,25 @@ -- Found htslib, version 1.20 -- Checking for module 'jansson' -- Found jansson, version 2.14 -[100%] Linking CXX static library libsdsl.a -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 Using installed libhandlegraph --- Configuring done (0.8s) --- Generating done (0.0s) +-- Configuring done (4.0s) +-- Generating done (0.1s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make -f CMakeFiles/test_libvgio.dir/build.make CMakeFiles/test_libvgio.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +/usr/bin/cmake -P CMakeFiles/test_libvgio.dir/cmake_clean.cmake +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -/usr/bin/cmake -P CMakeFiles/test_libvgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' @@ -15333,82 +15365,66 @@ make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 2%] Running cpp protocol buffer compiler on deps/vg.proto -[ 5%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto +[ 5%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" -cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -[ 14%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -[ 14%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -[ 14%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o -[ 23%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -[ 23%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o -[ 23%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -[ 29%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -[ 29%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o -[ 32%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include 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/build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp -[ 38%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp -[ 41%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/hfile_cppstream.cpp -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/edit.cpp.o -MF CMakeFiles/vgio_static.dir/src/edit.cpp.o.d -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/edit.cpp -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/json2pb.cpp -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/hfile_cppstream.cpp -[ 44%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 -[ 47%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_io.cpp -[ 52%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -[ 52%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 +[100%] Linking CXX static library libsdsl.a +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake +cd /build/reproducible-path/vg-1.59.0+ds/deps/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=" +[ 8%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o +[ 11%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_emitter.cpp -/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_emitter.cpp -[ 55%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o +[ 14%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o +[ 20%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o +[ 20%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_io.cpp -[ 58%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o +[ 23%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o +[ 26%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o +[ 32%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o +[ 32%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o +[ 35%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 +/usr/bin/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 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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 +[ 41%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +[ 44%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fPIC 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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 +[ 52%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o +/usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/stream.cpp.o -MF CMakeFiles/vgio.dir/src/stream.cpp.o.d -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream.cpp +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/vg.pb.cc.o -MF CMakeFiles/vgio_static.dir/vg.pb.cc.o.d -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/vg.pb.cc +[ 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 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'/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 @@ -15426,22 +15442,31 @@ make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C +[ 73%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o +[ 73%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o +/usr/bin/g++ 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-ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -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 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 +[ 79%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o +[ 82%] 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 make -f CMakeFiles/Makefile2 preinstall +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/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 make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' -g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp Install the project... /usr/bin/cmake -P cmake_install.cmake -ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o -- Install configuration: "Release" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vector_il.hpp @@ -15512,7 +15537,6 @@ -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/raster_img.hpp -ranlib sonLib.a -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rle_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sct.hpp @@ -15557,12 +15581,8 @@ -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libsdsl.a -rm *.o -mv sonLib.a ../lib/ -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm +[ 85%] 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/reproducible-path/vg-1.59.0+ds/include'. @@ -15573,112 +15593,100 @@ A cheat sheet in the extras/cheatsheet-directory. Have fun! . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gcsa2 && make directories && make lib/libgcsa2.a && mv lib/libgcsa2.a /build/reproducible-path/vg-1.59.0+ds/lib +cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C . ./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 +[ 88%] Building CXX 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -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 . ./source_me.sh && rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/reproducible-path/vg-1.59.0+ds/include:/build/reproducible-path/vg-1.59.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp" make && cp lib/libbdsg.a /build/reproducible-path/vg-1.59.0+ds/lib && cp -r bdsg/include/* /build/reproducible-path/vg-1.59.0+ds/include -rm -f lib/libxg.a -cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include -. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' +[ ! -e bdsg/obj ] || rm -r bdsg/obj +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' rm -rf bin lib obj -mkdir -p bin -mkdir -p lib -mkdir -p obj rm -f *.o *.a build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' -[ ! -e bdsg/obj ] || rm -r bdsg/obj +g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp cd tests && make clean -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp +[ ! -e lib ] || rm -r lib make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dbg.o src/dbg.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gcsa.o src/gcsa.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp rm -f test_bwtmerge test_metadata test_queries test_support test_variants *.o -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/lcp.o src/lcp.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_graph.o src/path_graph.cpp +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' +[ ! -e bin ] || rm -r bin make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' -[ ! -e lib ] || rm -r lib -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp +make[3]: 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/gbwt' mkdir -p bin -[ ! -e bin ] || rm -r bin -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' -mkdir -p lib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' +mkdir -p bin +mkdir -p lib +mkdir -p lib mkdir -p obj +ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o +mkdir -p obj +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o +ranlib sonLib.a +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/bwtmerge.o src/bwtmerge.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwt.o src/cached_gbwt.cpp +rm *.o +mv sonLib.a ../lib/ +gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 +[ 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 -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/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 +[ 94%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o +/usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio_static.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/vpkg.cpp +gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm +gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm +gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dynamic_gbwt.o src/dynamic_gbwt.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/fast_locate.o src/fast_locate.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dbg.o src/dbg.cpp mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/mapped_structs.cpp -o bdsg/obj/mapped_structs.o -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/bwtmerge.o src/bwtmerge.cpp mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/mapped_structs.cpp -o bdsg/obj/mapped_structs.o +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gcsa.o src/gcsa.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwt.o src/gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwt.o src/cached_gbwt.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata.o src/metadata.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/reference_path_overlay.cpp -o bdsg/obj/reference_path_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_reference_path_overlay.cpp -o bdsg/obj/packed_reference_path_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/path_subgraph_overlay.cpp -o bdsg/obj/path_subgraph_overlay.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/subgraph_overlay.cpp -o bdsg/obj/subgraph_overlay.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dynamic_gbwt.o src/dynamic_gbwt.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/fast_locate.o src/fast_locate.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwt.o src/gbwt.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata.o src/metadata.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/subgraph_overlay.cpp -o bdsg/obj/subgraph_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/test.o src/test.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/variants.o src/variants.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_gbwt.o src/build_gbwt.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I 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-I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/merge_gbwt.o src/merge_gbwt.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/benchmark.o src/benchmark.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata_tool.o src/metadata_tool.cpp -/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o mv ../bin/sonLibTests.tmp ../bin/sonLibTests +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/lcp.o src/lcp.cpp make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' -. ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/reproducible-path/vg-1.59.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/reproducible-path/vg-1.59.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/reproducible-path/vg-1.59.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' -cd externalTools && make all -make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' -cd threeEdgeConnected && make all -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' -gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c -ar rc 3EdgeConnected.a *.o -ranlib 3EdgeConnected.a +rm -f lib/libxg.a +cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include +. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp [ 97%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 -rm *.o -mv 3EdgeConnected.a ../..//../sonLib/lib/ -cp inc/*.h ../..//../sonLib/lib/ -gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_graph.o src/path_graph.cpp /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wl,--dependency-file,CMakeFiles/vgio.dir/link.d -Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/lib/x86_64-linux-gnu/libprotobuf.so -lhts -ljansson /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 97%] Built target vgio +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o [100%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' -make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' -gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I .//../sonLib/lib/ -c impl/*.c -gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/ranlib libvgio.a make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' @@ -15689,6 +15697,7 @@ make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg//CMakeFiles/progress.marks +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend @@ -15699,24 +15708,26 @@ make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/variants.o src/variants.cpp [ 0%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend -make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" -make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build -make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +[ 50%] Built target vgio +make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' -[100%] Built target vgio [100%] Built target vgio_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 @@ -15732,39 +15743,68 @@ -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include/vg -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/vpkg.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_internal.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/fdstream.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_cppstream.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_input_stream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/loader.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_output_stream.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_emitter.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream_multiplexer.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_internal.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/loader.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_io.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/gafkluge.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/edit.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_cppstream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_iterator.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/basic_stream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_iterator.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/vpkg.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/json2pb.h --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_emitter.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/fdstream.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/registry.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_emitter.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_emitter.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/gafkluge.hpp --- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/edit.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_iterator.hpp +-- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/registry.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' +. ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/reproducible-path/vg-1.59.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/reproducible-path/vg-1.59.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/reproducible-path/vg-1.59.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' +cd externalTools && make all +make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' +cd threeEdgeConnected && make all +make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' +gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_gbwt.o src/build_gbwt.cpp +ar rc 3EdgeConnected.a *.o +ranlib 3EdgeConnected.a +rm *.o +mv 3EdgeConnected.a ../..//../sonLib/lib/ +cp inc/*.h ../..//../sonLib/lib/ +gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm +make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' +make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' +gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -I inc -I .//../sonLib/lib/ -c impl/*.c +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_ri.o src/build_ri.cpp +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/merge_gbwt.o src/merge_gbwt.cpp +gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/benchmark.o src/benchmark.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata_tool.o src/metadata_tool.cpp +/usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' +rm -f lib/libbdsg.a +ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/mapped_structs.o bdsg/obj/packed_graph.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/reference_path_overlay.o bdsg/obj/packed_reference_path_overlay.o bdsg/obj/path_subgraph_overlay.o bdsg/obj/subgraph_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/snarl_distance_index.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o +ar: creating lib/libbdsg.a ar rcs lib/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 +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_gbwt obj/build_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_ri obj/build_ri.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/merge_gbwt obj/merge_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 @@ -15798,20 +15838,16 @@ /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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa2gbwt.o src/gfa2gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz_stats.o src/gbz_stats.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/kmer_freq.o src/kmer_freq.cpp -rm -f lib/libbdsg.a -ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/mapped_structs.o bdsg/obj/packed_graph.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/reference_path_overlay.o bdsg/obj/packed_reference_path_overlay.o bdsg/obj/path_subgraph_overlay.o bdsg/obj/subgraph_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/snarl_distance_index.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o -ar: creating lib/libbdsg.a -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' ar rcs lib/libgcsa2.a obj/algorithms.o obj/dbg.o obj/files.o obj/gcsa.o obj/internal.o obj/lcp.o obj/path_graph.o obj/support.o obj/utils.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' -ar rs lib/libxg.a deps/xg/xg.o -ar: creating lib/libxg.a ar rcs lib/libgbwtgraph.a obj/algorithms.o obj/cached_gbwtgraph.o obj/gbwtgraph.o obj/gbz.o obj/gfa.o obj/internal.o obj/minimizer.o obj/path_cover.o obj/utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/gfa2gbwt obj/gfa2gbwt.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/gbz_stats obj/gbz_stats.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/kmer_freq obj/kmer_freq.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 rm obj/kmer_freq.o obj/gbz_stats.o obj/gfa2gbwt.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' +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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp @@ -16116,8 +16152,6 @@ . ./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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp -. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp -. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:147:31: required from here @@ -16133,6 +16167,8 @@ /usr/include/google/protobuf/message_lite.h:381:7: note: declared here 381 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ +. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp +. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp @@ -16170,7 +16206,7 @@ . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -o bin/vg-sse3 obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/back_translate.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chain_items.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/component_paths.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gbwt_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_helpers.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/kff.o obj/unittest/kmp.o obj/unittest/locally_expand_graph.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/mem_accelerator.o obj/unittest/min_cut_graph.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/protobuf.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/sequence_complexity.o obj/unittest/snarl_distance_index.o obj/unittest/snarl_seed_clusterer.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/transcriptome.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chain_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/clip_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/haplotypes_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/options.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o obj/config/allocator_config_jemalloc.o -Wl,-z,relro -Wl,-z,now lib/libvg.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph -lfastahack -lhts -ltabixpp -lcairo -lm -ldl -lz -lz -lm -lz -lfontconfig -lz -lz -lm -lz -lbrotlicommon -lexpat -lm -lfreetype -lz -lbz2 -lpng16 -lz -lm -lz -lbrotlidec -lbrotlicommon -lX11 -lpthread -lxcb -lXau -lXext -lpthread -lxcb -lXau -lXrender -lX11 -lpthread -lxcb -lXau -lX11 -lpthread -lXau -lxcb -lXau -lxcb-render -lxcb -lXau -lxcb-shm -lxcb -lXau -lXdmcp -lpixman-1 -lm -pthread -lzstd -pthread -rdynamic -ldw -lelf -latomic "-lboost_program_options""" -ldl -llzma -lzstd /usr/lib/x86_64-linux-gnu/libjemalloc.a -Wl,-Bstatic -lvgio -lhts -ldeflate -lz -llzma -lprotobuf -lz -ljansson -Wl,-Bdynamic -lpthread -lm make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3" dh_auto_build -- SFX=-plain all test/build_graph bin/shuf - make -j42 "INSTALL=install --strip-program=true" SFX=-plain all test/build_graph bin/shuf + make -j20 "INSTALL=install --strip-program=true" SFX=-plain all test/build_graph bin/shuf make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC @@ -16220,8 +16256,8 @@ -- Looking for C++ include cstdio -- Looking for C++ include cstdio - found -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot --- Configuring done (1.4s) --- Generating done (0.2s) +-- Configuring done (11.6s) +-- Generating done (0.6s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 @@ -16237,64 +16273,64 @@ make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' -[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -[ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o -[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o -[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp -[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o +[ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bits.cpp -[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o +[ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o +[ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp -[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o +[ 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp -[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp +[ 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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/config.cpp -[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o +[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp +[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_config.cpp +[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_isa.cpp +[ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp +[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o +[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa.cpp -[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_isa.cpp +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp +[ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/io.cpp +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp -[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_config.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 +[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/memory_management.cpp +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/io.cpp -[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_fs.cpp -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/louds_tree.cpp -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o +[ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sd_vector.cpp +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sfstream.cpp -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o -MF CMakeFiles/sdsl.dir/simple_sds.cpp.o.d -o CMakeFiles/sdsl.dir/simple_sds.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/simple_sds.cpp -[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o +[ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/structure_tree.cpp -cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/wt_helper.cpp -[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint128_t.cpp +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp +[ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o +cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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 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: @@ -16471,66 +16507,66 @@ . ./source_me.sh && rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/reproducible-path/vg-1.59.0+ds/include:/build/reproducible-path/vg-1.59.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" make && cp lib/libbdsg.a /build/reproducible-path/vg-1.59.0+ds/lib && cp -r bdsg/include/* /build/reproducible-path/vg-1.59.0+ds/include rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include -. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' make[3]: Nothing to be done for 'directories'. make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' -rm -rf bin lib obj +. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' -[ ! -e bdsg/obj ] || rm -r bdsg/obj +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' 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 +rm -rf bin lib obj +[ ! -e bdsg/obj ] || rm -r bdsg/obj [ ! -e lib ] || rm -r lib rm -f *.o *.a build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq -[ ! -e bin ] || rm -r bin cd tests && make clean -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' -make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' +[ ! -e bin ] || rm -r bin make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' rm -f test_bwtmerge test_metadata test_queries test_support test_variants *.o +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' +make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' mkdir -p bin mkdir -p lib -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o mkdir -p obj -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/bwtmerge.o src/bwtmerge.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/mapped_structs.cpp -o bdsg/obj/mapped_structs.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwt.o src/cached_gbwt.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dynamic_gbwt.o src/dynamic_gbwt.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/fast_locate.o src/fast_locate.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/reference_path_overlay.cpp -o bdsg/obj/reference_path_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwt.o src/gbwt.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_reference_path_overlay.cpp -o bdsg/obj/packed_reference_path_overlay.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/path_subgraph_overlay.cpp -o bdsg/obj/path_subgraph_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata.o src/metadata.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/subgraph_overlay.cpp -o bdsg/obj/subgraph_overlay.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/test.o src/test.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/mapped_structs.cpp -o bdsg/obj/mapped_structs.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/variants.o src/variants.cpp -g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o +make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_gbwt.o src/build_gbwt.cpp +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_ri.o src/build_ri.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/merge_gbwt.o src/merge_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/benchmark.o src/benchmark.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata_tool.o src/metadata_tool.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp -make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/reference_path_overlay.cpp -o bdsg/obj/reference_path_overlay.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_reference_path_overlay.cpp -o bdsg/obj/packed_reference_path_overlay.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/path_subgraph_overlay.cpp -o bdsg/obj/path_subgraph_overlay.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/subgraph_overlay.cpp -o bdsg/obj/subgraph_overlay.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o +g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o ar rcs lib/libgbwt.a obj/algorithms.o obj/bwtmerge.o obj/cached_gbwt.o obj/dynamic_gbwt.o obj/fast_locate.o obj/files.o obj/gbwt.o obj/internal.o obj/metadata.o obj/support.o obj/test.o obj/utils.o obj/variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_gbwt obj/build_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_ri obj/build_ri.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 @@ -16881,6 +16917,7 @@ . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp +. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp 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 @@ -16896,7 +16933,6 @@ /usr/include/google/protobuf/message_lite.h:381:7: note: declared here 381 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ -. ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp @@ -16947,7 +16983,7 @@ debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_build -- docs - make -j42 "INSTALL=install --strip-program=true" docs + make -j20 "INSTALL=install --strip-program=true" docs make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC @@ -20422,2434 +20458,8756 @@ ; done Testing /build/reproducible-path/vg-1.59.0+ds/debian/help/vg-avx2 '/build/reproducible-path/vg-1.59.0+ds/debian/help/vg-avx2' -> '/build/reproducible-path/vg-1.59.0+ds/debian/help/vg' -index file /tmp/vg-KIisg5/vg-zUcrka.fai not found, generating... -index file /tmp/vg-KIisg5/vg-ic41h7.fai not found, generating... -index file /tmp/vg-KIisg5/vg-gnIBPd.fai not found, generating... -index file /tmp/vg-KIisg5/vg-tEGA1U.fai not found, generating... -warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;CIPOS=0,3;CIEND=-3,0 GT ! -index file /tmp/vg-KIisg5/vg-iAbLwN.fai not found, generating... -index file /tmp/vg-KIisg5/vg-t94QNv.fai not found, generating... -index file /tmp/vg-KIisg5/vg-J1uKQ2.fai not found, generating... -index file /tmp/vg-KIisg5/vg-A16SLv.fai not found, generating... -index file /tmp/vg-KIisg5/vg-4edqAi.fai not found, generating... -index file /tmp/vg-KIisg5/vg-9wJwx3.fai not found, generating... -index file /tmp/vg-KIisg5/vg-B8tGnA.fai not found, generating... -index file /tmp/vg-KIisg5/vg-XfpseM.fai not found, generating... -index file /tmp/vg-KIisg5/vg-cnFDbp.fai not found, generating... -index file /tmp/vg-KIisg5/vg-dKFZi0.fai not found, generating... -Warning: deletion END and SVLEN do not agree [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;SVLEN=-19;CIPOS=0,3;CIEND=-3,0;SPAN=19 GT -END: 29 SVLEN: -19 -warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;SVLEN=-19;CIPOS=0,3;CIEND=-3,0;SPAN=19 GT -index file /tmp/vg-KIisg5/vg-2juJJE.fai not found, generating... -Warning: deletion END and SVLEN do not agree [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;SVLEN=-19;CIPOS=0,3;CIEND=-3,0;SPAN=19 GT -END: 29 SVLEN: -19 -warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;SVLEN=-19;CIPOS=0,3;CIEND=-3,0;SPAN=19 GT -index file /tmp/vg-KIisg5/vg-oI02Of.fai not found, generating... -index file /tmp/vg-KIisg5/vg-d44ywN.fai not found, generating... -index file /tmp/vg-KIisg5/vg-IvNRes.fai not found, generating... -index file /tmp/vg-KIisg5/vg-ApgW4Q.fai not found, generating... -index file /tmp/vg-KIisg5/vg-HeS1yX.fai not found, generating... -index file /tmp/vg-KIisg5/vg-4wCKwu.fai not found, generating... -index file /tmp/vg-KIisg5/vg-QV4G1Y.fai not found, generating... -index file /tmp/vg-KIisg5/vg-zsw1pW.fai not found, generating... -index file /tmp/vg-KIisg5/vg-aj4xfB.fai not found, generating... -Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=18;CIPOS=0,3;SPAN=4 GT -END: 18 POS: 9 -warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=18;CIPOS=0,3;SPAN=4 GT -index file /tmp/vg-KIisg5/vg-p5wpc2.fai not found, generating... -Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=18;CIPOS=0,3;SPAN=4 GT -END: 18 POS: 9 -warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=18;CIPOS=0,3;SPAN=4 GT -index file /tmp/vg-KIisg5/vg-Z3ZSw9.fai not found, generating... -Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=13;CIPOS=0,3;SPAN=4 GT -END: 13 POS: 9 -Warning: VCF writer incorrecty produced END = POS + SVLEN for an insertion. Fixing END to POS. -index file /tmp/vg-KIisg5/vg-l3Qqmo.fai not found, generating... -Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=13;CIPOS=0,3;SPAN=4 GT -END: 13 POS: 9 -Warning: VCF writer incorrecty produced END = POS + SVLEN for an insertion. Fixing END to POS. -index file /tmp/vg-KIisg5/vg-W6UOQz.fai not found, generating... -index file /tmp/vg-KIisg5/vg-7ZqOHN.fai not found, generating... -index file /tmp/vg-KIisg5/vg-wUHsKm.fai not found, generating... -index file /tmp/vg-KIisg5/vg-U2aHcD.fai not found, generating... -warning:[vg::Constructor] Lowercase characters found in x; coercing to uppercase. -index file /tmp/vg-KIisg5/vg-rupNfA.fai not found, generating... -warning:[vg::Constructor] Lowercase characters found in x; coercing to uppercase. -index file /tmp/vg-KIisg5/vg-tWiHrs.fai not found, generating... -index file /tmp/vg-KIisg5/vg-x5rwwP.fai not found, generating... -index file /tmp/vg-KIisg5/vg-GlcFup.fai not found, generating... -index file /tmp/vg-KIisg5/vg-ixQ3GM.fai not found, generating... -2 0 -3 0 -iterated on 4 0 -iterated on 5 0 -iterated on 7 0 -iterated on 8 0 -iterated on 7 1 -Warning: Cactus does not currently support finding snarls in a single-node connected component -warning:[GFAParser] Skipping GFA P line: GFA format error: On pass 2: On line 2: Duplicate path x exists in graph -Testing libvgio... -warning: distance index uses oversized snarls, which may make mapping slow - try increasing --snarl-limit when building the distance index -warning: distance index uses oversized snarls, which may make mapping slow - try increasing --snarl-limit when building the distance index -warning: distance index uses oversized snarls, which may make mapping slow - try increasing --snarl-limit when building the distance index -warning: distance index uses oversized snarls, which may make mapping slow - try increasing --snarl-limit when building the distance index -12 -11 - WARNING: Excluded 2 transcripts with overlapping exons or incorrect exon order. - WARNING: Excluded 2 transcripts with overlapping exons or incorrect exon order. - WARNING: Excluded 1 transcripts with exon overlapping a haplotype break. +t/00_unittest.t: line 12: 3281926 Illegal instruction vg test t/00_unittest.t ....... 1..1 -=============================================================================== -All tests passed (8336883 assertions in 617 test cases) -ok 1 - vg unit tests complete successfully -ok +not ok 1 - vg unit tests complete successfully +# got: '132' +# expected: '0' +Failed 1/1 subtests t/01_build_graph.t .... 1..1 ok 1 - graph building with the API ok -warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;END=1017354;NS=2504;SVLEN=-3562;SVTYPE=DEL;DP=15541;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0 ! -warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AN=5008;CS=ALU_umary;MEINFO=AluUndef,2,281,+;NS=2504;SVLEN=279;SVTYPE=ALU;TSD=null;DP=18053;EAS_AF=0;AMR_AF=0.0043;AFR_AF=0.0303;EUR_AF=0;SAS_AF=0 ! -warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 490168 DUP_gs_CNV_20_1490168_1549769 G 100 PASS AC=1;AF=0.000199681;AN=5008;CS=DUP_gs;END=1549769;NS=2504;SVTYPE=DUP;DP=21874;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0.001 ! -Warning: deletion END and SVLEN do not agree [canonicalize] z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;END=1017354;NS=2504;SVLEN=-3562;SVTYPE=DEL;DP=15541;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0;SPAN=3562 -END: 1017354 SVLEN: -3562 -warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;END=1017354;NS=2504;SVLEN=-3562;SVTYPE=DEL;DP=15541;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0;SPAN=3562 -Warning: deletion END and SVLEN do not agree [canonicalize] z 43039 UW_VH_8960 T 100 PASS AC=2;AF=0.000399361;AN=5008;CIEND=0,208;CIPOS=-245,0;CS=DEL_union;END=1044489;NS=2504;SVLEN=-1677;SVTYPE=DEL;DP=18239;EAS_AF=0;AMR_AF=0.0029;AFR_AF=0;EUR_AF=0;SAS_AF=0;SPAN=1677 -END: 1044489 SVLEN: -1677 -Warning: deletion END and SVLEN do not agree [canonicalize] z 73265 UW_VH_16869 G 100 PASS AC=3;AF=0.000599042;AN=5008;CIEND=0,102;CIPOS=-125,0;CS=DEL_union;END=1077324;NS=2504;SVLEN=-4157;SVTYPE=DEL;DP=19418;EAS_AF=0;AMR_AF=0;AFR_AF=0.0023;EUR_AF=0;SAS_AF=0;SPAN=4157 -END: 1077324 SVLEN: -4157 -Warning: deletion END and SVLEN do not agree [canonicalize] z 129960 BI_GS_DEL1_B3_P2734_8 A 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-16,16;CIPOS=-16,16;CS=DEL_union;END=1131366;NS=2504;SVLEN=-1405;SVTYPE=DEL;DP=18804;EAS_AF=0;AMR_AF=0;AFR_AF=0.0008;EUR_AF=0;SAS_AF=0;SPAN=1405 -END: 1131366 SVLEN: -1405 -Warning: deletion END and SVLEN do not agree [canonicalize] z 307697 UW_VH_6096 A 100 PASS AC=2;AF=0.000399361;AN=5008;CIEND=0,82;CIPOS=-77,0;CS=DEL_union;END=1318064;NS=2504;SVLEN=-10447;SVTYPE=DEL;DP=20245;EAS_AF=0.002;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0;SPAN=10447 -END: 1318064 SVLEN: -10447 -Warning: deletion END and SVLEN do not agree [canonicalize] z 389096 UW_VH_3735 G 100 PASS AC=2647;AF=0.528554;AN=5008;CIEND=0,478;CIPOS=-443,0;CS=DEL_union;END=1390815;NS=2504;SVLEN=-2051;SVTYPE=DEL;DP=18400;EAS_AF=0.7996;AMR_AF=0.5922;AFR_AF=0.2685;EUR_AF=0.5;SAS_AF=0.5849;SPAN=2051 -END: 1390815 SVLEN: -2051 -Warning: deletion END and SVLEN do not agree [canonicalize] z 405367 BI_GS_DEL1_B3_P2734_19 G 100 PASS AC=2;AF=0.000399361;AN=5008;CIEND=-9,9;CIPOS=-9,9;CS=DEL_union;END=1406601;NS=2504;SVLEN=-1232;SVTYPE=DEL;DP=21506;EAS_AF=0;AMR_AF=0;AFR_AF=0.0015;EUR_AF=0;SAS_AF=0;SPAN=1232 -END: 1406601 SVLEN: -1232 -Warning: deletion END and SVLEN do not agree [canonicalize] z 557325 UW_VH_21401 G 100 PASS AC=314;AF=0.0626997;AN=5008;CIEND=0,245;CIPOS=-268,0;CS=DEL_union;END=1559946;NS=2504;SVLEN=-2877;SVTYPE=DEL;DP=17241;EAS_AF=0.004;AMR_AF=0.0648;AFR_AF=0.0552;EUR_AF=0.1412;SAS_AF=0.0511;SPAN=2877 -END: 1559946 SVLEN: -2877 -Warning: deletion END and SVLEN do not agree [canonicalize] z 560739 YL_CN_CHB_4219 T 100 PASS AC=4099;AF=0.81849;AN=5008;CIEND=-500,1000;CIPOS=-1000,500;CS=DEL_union;END=1593685;NS=2504;SVLEN=-32947;SVTYPE=DEL;DP=20713;EAS_AF=0.7867;AMR_AF=0.6527;AFR_AF=0.9213;EUR_AF=0.7903;SAS_AF=0.8589;SPAN=32947 -END: 1593685 SVLEN: -32947 -Warning: deletion END and SVLEN do not agree [canonicalize] z 596789 BI_GS_DEL1_B1_P2734_566 C 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-11,11;CIPOS=-11,11;CS=DEL_union;END=1600144;NS=2504;SVLEN=-3354;SVTYPE=DEL;DP=16771;EAS_AF=0.001;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0;SPAN=3354 -END: 1600144 SVLEN: -3354 -Warning: deletion END and SVLEN do not agree [canonicalize] z 599361 BI_GS_DEL1_B2_P2734_449 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-20,20;CIPOS=-20,20;CS=DEL_union;END=1605179;NS=2504;SVLEN=-5817;SVTYPE=DEL;DP=17612;EAS_AF=0;AMR_AF=0;AFR_AF=0.0008;EUR_AF=0;SAS_AF=0;SPAN=5817 -END: 1605179 SVLEN: -5817 -Warning: deletion END and SVLEN do not agree [canonicalize] z 602412 BI_GS_DEL1_B4_P2734_149 C 100 PASS AC=4;AF=0.000798722;AN=5008;CIEND=-15,15;CIPOS=-15,15;CS=DEL_union;END=1603204;NS=2504;SVLEN=-791;SVTYPE=DEL;DP=21930;EAS_AF=0.002;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0.002;SPAN=791 -END: 1603204 SVLEN: -791 -Warning: deletion END and SVLEN do not agree [canonicalize] z 670381 UW_VH_15556 T 100 PASS AC=14;AF=0.00279553;AN=5008;CIEND=0,256;CIPOS=-240,0;CS=DEL_union;END=1674237;NS=2504;SVLEN=-4037;SVTYPE=DEL;DP=18965;EAS_AF=0;AMR_AF=0;AFR_AF=0.0106;EUR_AF=0;SAS_AF=0;SPAN=4037 -END: 1674237 SVLEN: -4037 -Warning: deletion END and SVLEN do not agree [canonicalize] z 995483 UW_VH_2849 T 100 PASS AC=193;AF=0.0385383;AN=5008;CIEND=0,386;CIPOS=-423,0;CS=DEL_union;END=1997552;NS=2504;SVLEN=-2301;SVTYPE=DEL;DP=16520;EAS_AF=0;AMR_AF=0.0461;AFR_AF=0.0454;EUR_AF=0.0547;SAS_AF=0.047;SPAN=2301 -END: 1997552 SVLEN: -2301 -error:[vg::Constructor] On z, adding reference to last edit end, next end is at 1053404 but reference is only 459552 long -warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;END=1017354;NS=2504;SVLEN=-3562;SVTYPE=DEL;DP=15541;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0 ! -warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AN=5008;CS=ALU_umary;MEINFO=AluUndef,2,281,+;NS=2504;SVLEN=279;SVTYPE=ALU;TSD=null;DP=18053;EAS_AF=0;AMR_AF=0.0043;AFR_AF=0.0303;EUR_AF=0;SAS_AF=0 ! -Restricting to gi|568815592:29791752-29792749 from 1 to end -index file sv/x.fa.fai not found, generating... -index file tiny/ambiguous.fa.fai not found, generating... -warning:[vg::Constructor] Unsupported IUPAC ambiguity codes found in x; coercing to N. +t/02_vg_construct.t: line 18: 3281949 Illegal instruction vg construct -m 1000 -r 1mb1kgp/z.fa -v 1mb1kgp/z.vcf.gz > z.vg +t/02_vg_construct.t: line 28: 3281961 Illegal instruction vg construct -r 1mb1kgp/z.fa -v 1mb1kgp/z.vcf.gz -S > /dev/null +t/02_vg_construct.t: line 35: 3281968 Illegal instruction vg construct -m 1000 -r complex/c.fa -v complex/c.vcf.gz > c.vg +t/02_vg_construct.t: line 51: 3281986 Illegal instruction vg construct -r order/n.fa -v order/z.vcf.gz -R n:47-73 > /dev/null +t/02_vg_construct.t: line 74: 3283614 Illegal instruction vg construct -r 1mb1kgp/z.fa -v 1mb1kgp/z.vcf.gz -R z:10-20 > /dev/null +t/02_vg_construct.t: line 101: 3283955 Illegal instruction vg construct -r small/x.fa > /dev/null +t/02_vg_construct.t: line 113: 3283984 Illegal instruction vg construct -r small/x.fa -v small/x.v4.3.vcf.gz > x.vg 2> log.txt +t/02_vg_construct.t: line 119: 3283987 Illegal instruction vg construct -r tiny/ambiguous.fa > tiny.vg t/02_vg_construct.t ... 1..30 -ok 1 - construction produces the right number of nodes -ok 2 - construction produces the right number of edges -ok 3 - construction obeys rename and region options -ok 4 - construction of a 1 megabase graph from the 1000 Genomes succeeds -ok 5 - the 1mb graph has the expected number of nodes -ok 6 - the 1mb graph has the expected number of edges +not ok 1 - unnamed test +# got: '210' +# expected: 'construction produces the right number of nodes' +not ok 2 - unnamed test +# got: '291' +# expected: 'construction produces the right number of edges' +not ok 3 - unnamed test +# got: '2' +# expected: 'construction obeys rename and region options' +not ok 4 - construction of a 1 megabase graph from the 1000 Genomes succeeds +# got: '132' +# expected: '0' +not ok 5 - unnamed test +# got: '84559' +# expected: 'the 1mb graph has the expected number of nodes' +not ok 6 - unnamed test +# got: '115375' +# expected: 'the 1mb graph has the expected number of edges' not ok 7 - vg construct can skip self-inconsistent structural variants +# got: '132' +# expected: '0' +ok 8 - node size is manageable by default +not ok 9 - construction of a very complex region succeeds +# got: '132' +# expected: '0' +not ok 10 - unnamed test +# got: '71' +# expected: 'the complex graph has the expected number of nodes' +not ok 11 - unnamed test +# got: '116' +# expected: 'the complex graph has the expected number of edges' +ok 12 - the ordering of variants at the same position has no effect on the resulting graph +not ok 13 - construction does not fail when the first position in the VCF is repeated and has an indel +# got: '132' +# expected: '0' +ok 14 - the size of the regions used in construction has no effect on the graph +ok 15 - the number of threads used in construction has no effect on the graph +ok 16 - the number of threads and regions used in construction has no effect on the graph +not ok 17 - construction of a graph with two head nodes succeeds +# got: '132' +# expected: '0' +not ok 18 - unnamed test +# got: '1074' +# expected: 'the graph contains all the sequence in the reference and VCF' +not ok 19 - varying the max node size does not affect graph length +# got: '0' +# expected: '1' +not ok 20 - unnamed test +# got: '12' +# expected: 'nodes are correctly capped in size' +not ok 21 - unnamed test +# got: '241' +# expected: '-R --region flag is respected' +not ok 22 - vg construct does not require a vcf +# got: '132' +# expected: '0' +ok 23 - vg construct respects node size limit +not ok 24 - --region can be interpreted to be a reference sequence (and not parsed as a region spec) +# got: '0' +# expected: '1' +not ok 25 - vg constructs the correct graph for inversions +# got: 'd41d8cd98f00b204e9800998ecf8427e' +# expected: '9f7d23d3c5382229c6c3bf64d1ba44bc' +not ok 26 - vg construct skips variants with . ALTs +# got: '' +# expected: '1' +not ok 27 - VCF with * alleles is accepted +# got: '132' +# expected: '0' +not ok 28 - VCF record with * allele is rejected +# got: '1' +# expected: '0' +not ok 29 - Reference with ambiguity codes has them coerced to Ns +# got: '132' +# expected: '0' +not ok 30 - Expected number of Ns are created +# got: '0' +# expected: '10' +Failed 24/30 subtests +t/03_vg_view.t: line 24: 3284049 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz + 3284050 | vg view -Vg - + 3284051 | vg view -Fv - > x.vg +t/03_vg_view.t: line 48: 3284088 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz + 3284089 | vg view -v - > x.vg +t/03_vg_view.t: line 55: 3284100 Illegal instruction vg view -Fv overlaps/two_snvs_assembly1.gfa > /dev/null 2> errors.txt +t/03_vg_view.t: line 59: 3284105 Illegal instruction vg view -Fv overlaps/incorrect_overlap.gfa > /dev/null 2> errors.txt +t/03_vg_view.t: line 65: 3284111 Illegal instruction vg paths -M -x test/graphs/rgfa_with_reference.rgfa > paths.truth.txt +t/03_vg_view.t: line 66: 3284112 Illegal instruction vg view test/graphs/rgfa_with_reference.rgfa + 3284113 | vg paths -M -x - > paths.test.txt +t/03_vg_view.t: line 70: 3284115 Illegal instruction vg paths -M -x test/graphs/gfa_with_reference.gfa > paths.truth.txt +t/03_vg_view.t: line 71: 3284116 Illegal instruction vg view test/graphs/gfa_with_reference.gfa + 3284117 | vg paths -M -x - > paths.test.txt +t/03_vg_view.t: line 77: 3284120 Illegal instruction vg view graphs/hap_subrange.gfa > /dev/null +t/03_vg_view.t ........ +1..23 +not ok 1 - view produces the expected number of lines of dot output +# got: '0' +# expected: '505' +not ok 2 - view produces the expected number of lines of GFA output +# got: '0' +# expected: '503' +not ok 3 - view converts back and forth between GFA and vg format +# got: '0' +# expected: '10' +not ok 4 - view can convert BAM to GAM +# got: '0' +# expected: '3333' +ok 5 - view can round-trip JSON and GAM +not ok 6 - view can round-trip qualities and encodes tham as PHRED+0 base-64-encoded strings in JSON +# got: 'FFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIBBII''''IIIIII'F'IIIIIIII'FIIIIIIIIFFIIIFIIIIIIIFIIIIIIIIIIFIIFIIIIIIIIIIIIIIIIIIIIFIIFIIIFIIIFIIIIIFIIIIIII' +# expected: '' +ok 7 - view can reconstruct a VG graph from JSON +ok 8 - view can pass through VG when loading as vg::VG +ok 9 - view can pass through semantically identical VG normally +ok 10 - view parses sample names +not ok 11 - view can handle fastq input +# got: '0' +# expected: '2000' +not ok 12 - unnamed test +# got: '4' +# expected: 'view can translate graphs with 2-node cycles' +not ok 13 - view outputs properly oriented GFA +# got: '0' +# expected: '1' +not ok 14 - view produces the expected number of lines of dot output from a cyclic graph +# got: '0' +# expected: '23' +not ok 15 - streaming JSON output produces the expected number of chunks +# got: '0' +# expected: '4' +ok 16 - duplicate warnings can be suppressed when loading as vg::VG +not ok 17 - gfa graphs with overlaps are rejected +# got: '132' +# expected: '1' +not ok 18 - GFA import produces a concise error message when overlaps are present +# got: '0' +# expected: '2' +not ok 19 - GFA import rejects a GFA file with an overlap that goes beyond its sequences +# got: '132' +# expected: '1' +not ok 20 - GFA import produces a concise error message in that case +# got: '0' +# expected: '2' +ok 21 - vg view preserves path metadata of rGFA file +ok 22 - vg view preserves path metadata of GFA file +not ok 23 - vg view can emit a GFA file with subranges on a haplotype without explicit phase blocks +# got: '132' +# expected: '0' +Failed 15/23 subtests +t/04_vg_align.t: line 10: 3284122 Illegal instruction vg construct -m 1000 -r small/x.fa -v small/x.vcf.gz > x.vg +t/04_vg_align.t: line 38: 3284168 Illegal instruction vg construct -m 1000 -r tiny/tiny.fa > t.vg +t/04_vg_align.t: line 40: 3284169 Illegal instruction vg align -s $seq t.vg + 3284170 | vg augment t.vg - -i -S > t2.vg +t/04_vg_align.t: line 47: 3284186 Illegal instruction vg align -s ACGT -j cyclic/reverse_self.vg > /dev/null +t/04_vg_align.t: line 50: 3284187 Illegal instruction vg align -s AGTCCTTGAAAGAGGGCAAAATAAACTGTTAGTAGAGCCAGGTCTGAAAACAACACTTTCTTGC inverting/m.vg > /dev/null +t/04_vg_align.t: line 53: 3284188 Illegal instruction vg align -s ATTTTTAACTCCATGTTTGAGAAACATTTAATAATGTAATGTGTTTGTGGCACAGCAGGAGTAC graphs/difficult-inv.vg > /dev/null +t/04_vg_align.t: line 56: 3284189 Illegal instruction vg align -s AAACATACATTTTC graphs/exploding.vg > /dev/null +t/04_vg_align.t ....... +1..20 +not ok 1 - alignment traverses the correct path +# got: '0' +# expected: '4' +not ok 2 - unnamed test +# got: '48' +# expected: 'alignment score is as expected' +not ok 3 - unnamed test +# got: '58' +# expected: 'full length bonus works and is included by default' +not ok 4 - unnamed test +# got: '37' +# expected: 'bonuses are included on only one end for pinned alignments' +not ok 5 - unnamed test +# got: '96' +# expected: 'scoring parameters are respected' +not ok 6 - unnamed test +# got: '96' +# expected: 'score-matrix file should give same results as --match 2 --mismatch 2: scoring parameters are respected' +not ok 7 - unnamed test +# got: '70211814' +# expected: 'alignment does not contain excessive soft clips under lenient scoring' +not ok 8 - unnamed test +# got: '70211814' +# expected: 'score-matrix file should give same results as --match 2 --mismatch 2: alignment does not contain excessive soft clips under lenient scoring' +not ok 9 - unnamed test +# got: '274' +# expected: 'alignment score does not overflow at 255 when using 8x16bit vectors' +not ok 10 - unnamed test +# got: '274' +# expected: 'score-matrix file should give same results as --match 2 --mismatch 2: alignment score does not overflow at 255 when using 8x16bit vectors' +not ok 11 - unnamed test +# got: '280136076' +# expected: 'Ns do not cause excessive soft clipping' +not ok 12 - unnamed test +# got: '59867694' +# expected: 'nodes are only referenced if they have mappings' +not ok 13 - align can use query names and outputs GAM +# got: '0' +# expected: '4' +not ok 14 - alignment to cyclic graphs works +# got: '0' +# expected: '1' +not ok 15 - graphs where duplicated nodes need flipping can be used for alignment +# got: '132' +# expected: '0' +not ok 16 - node flipping doesn't destroy the alignment +# got: '132' +# expected: '0' +not ok 17 - alignment correctly handles an inversion +# got: '132' +# expected: '0' +not ok 18 - the exploding graph doesn't blow up +# got: '132' +# expected: '0' +not ok 19 - unnamed test +# got: '1' +# expected: 'pinning doesn't cause problems for gssw' +not ok 20 - unnamed test +# got: '1' +# expected: 'left pinning is correctly handled' +Failed 20/20 subtests +t/05_vg_find.t: line 10: 3284197 Illegal instruction vg construct -m 1000 -r small/x.fa -v small/x.vcf.gz > x.vg +t/05_vg_find.t: line 13: 3284198 Illegal instruction vg index -x x.xg x.vg 2> /dev/null +t/05_vg_find.t: line 18: 3284209 Illegal instruction vg index -x x.xg -g x.gcsa -k 16 x.vg +t/05_vg_find.t: line 21: 3284216 Illegal instruction vg index -x x.xg -g x.gcsa -k 16 x.vg +t/05_vg_find.t: line 33: 3284232 Illegal instruction vg index -x m.xg inverting/m.vg +rm: cannot remove 'm.xg': No such file or directory +t/05_vg_find.t: line 38: 3284244 Illegal instruction vg construct -m 1000 -rmem/h.fa > h.vg +t/05_vg_find.t: line 39: 3284245 Illegal instruction vg index -g h.gcsa -k 16 h.vg +t/05_vg_find.t: line 43: 3284248 Illegal instruction vg construct -m 1000 -r minigiab/q.fa -v minigiab/NA12878.chr22.tiny.giab.vcf.gz -m 64 > giab.vg +t/05_vg_find.t: line 44: 3284249 Illegal instruction vg index -x giab.xg -g giab.gcsa -k 11 giab.vg +t/05_vg_find.t: line 61: 3284266 Illegal instruction vg construct -m 1000 -r small/x.fa -v small/x.vcf.gz > x.vg +t/05_vg_find.t: line 62: 3284267 Illegal instruction vg index -x x.xg -g x.gcsa -k 11 x.vg +t/05_vg_find.t: line 63: 3284268 Illegal instruction vg map -x x.xg -g x.gcsa -T small/x-s1337-n100.reads > x.gam +t/05_vg_find.t: line 65: 3284269 Illegal instruction vg gamsort -i x.sorted.gam.gai x.gam > x.sorted.gam +t/05_vg_find.t: line 75: 3284287 Illegal instruction vg construct -m 1000 -r tiny/tiny.fa -v tiny/tiny.vcf.gz > tiny.vg +t/05_vg_find.t: line 76: 3284288 Illegal instruction vg index -x tiny.xg tiny.vg +t/05_vg_find.t: line 84: 3284300 Done echo '{"node": [{"id": 1, "sequence": "A"}, {"id": 2, "sequence": "A"}], "edge": [{"from": 1, "to": 2}], "path": [{"name": "ref", "mapping": [{"position": {"node_id": 1}}]}]}' + 3284301 Illegal instruction | vg view -Jv - > test.vg +t/05_vg_find.t: line 85: 3284302 Illegal instruction vg index -x test.xg test.vg +t/05_vg_find.t: line 90: 3284308 Illegal instruction vg construct -m 1000 -r small/xy.fa -v small/xy2.vcf.gz -R x -C -a 2> /dev/null + 3284309 | vg view -j - + 3284310 Done | sed s/_alt/alt/g + 3284311 | vg view -Jv - > w.vg +t/05_vg_find.t: line 91: 3284312 Illegal instruction vg index -x w.xg w.vg +t/05_vg_find.t: line 92: 3284313 Done cat w.vg + 3284314 Illegal instruction | vg paths -d -v - > part1.tmp +t/05_vg_find.t: line 93: 3284315 Illegal instruction vg find -x w.xg -Q alt > part2.tmp +t/05_vg_find.t: line 97: 3284325 Illegal instruction vg construct -r tiny/tiny.fa -v tiny/tiny.vcf.gz > t.vg +t/05_vg_find.t: line 98: 3284326 Illegal instruction vg index -x t.xg t.vg +t/05_vg_find.t: line 101: 3284332 Illegal instruction vg find -x t.xg -E -p x:30-35 -p x:10-20 -W t. +t/05_vg_find.t: line 102: 3284336 Illegal instruction vg view t.x:30:35.vg +t/05_vg_find.t: line 106: 3284341 Illegal instruction vg find -x t.xg -E -R t.bed -W q. +t/05_vg_find.t: line 107: 3284346 Illegal instruction vg view q.x:10:20.vg +t/05_vg_find.t: line 107: 3284351 Illegal instruction vg view t.x:10:20.vg +t/05_vg_find.t: line 113: 3284356 Illegal instruction vg construct -r small/xy.fa -v small/xy2.vcf.gz -R x -C -a > x.vg 2> /dev/null +t/05_vg_find.t: line 114: 3284357 Illegal instruction vg index -x x.xg x.vg +t/05_vg_find.t: line 115: 3284358 Illegal instruction vg index -G x.gbwt -v small/xy2.vcf.gz x.vg +t/05_vg_find.t: line 126: 3284376 Illegal instruction vg construct -m 32 -r small/xy.fa -v small/xy2.vcf.gz -R x -C -a > x.vg 2> /dev/null +t/05_vg_find.t: line 127: 3284377 Illegal instruction vg index -G x.gbwt -v small/xy2.vcf.gz x.vg +t/05_vg_find.t: line 128: 3284378 Illegal instruction vg prune -u -m x.mapping -g x.gbwt -e 1 x.vg > x.unfolded.vg +t/05_vg_find.t: line 137: 3284380 Illegal instruction vg find -n 5 -n 23 --mapping x.mapping -x x.unfolded.vg 2> /dev/null + 3284381 | vg view -g - > found.gfa +cmp: EOF on found.gfa which is empty +t/05_vg_find.t ........ +1..29 +not ok 1 - construction +# got: '132' +# expected: '0' +not ok 2 - unnamed test +# got: '72' +# expected: 'a path can be queried from the xg index' +not ok 3 - a node near another can be obtained using context from the xg index +# got: '0' +# expected: '1' +not ok 4 - each perfect read contains one maximal exact match +# got: '0' +# expected: '100' +not ok 5 - unnamed test +# got: '8' +# expected: 'vg find -D finds approximate distance between 2 adjacent node starts' +not ok 6 - unnamed test +# got: '8' +# expected: 'vg find -D finds approximate distance between node start and adjacent snp' +not ok 7 - unnamed test +# got: '7' +# expected: 'vg find -D jumps deletion' +not ok 8 - unnamed test +# got: '7' +# expected: 'vg find -D jumps deletion from other allele in snp' +not ok 9 - vg find -L finds same number of nodes (with -c 1) +# got: '0' +# expected: '5' +not ok 10 - vg find -L works with -r. it scans from start position of first node in range +# got: '0' +# expected: '3' +not ok 11 - vg find -L tracks length from start position of input node +# got: '0' +# expected: '5' +not ok 12 - vg find -L works with more than one input node +# got: '0' +# expected: '7' +not ok 13 - unnamed test +# got: '[["ACC",["1:-32"]],["CCGTTAG",["1:5"]],["GTTAGAGT",["1:19"]],["TAGAGTCAG",["1:40"]]]' +# expected: 'we find the 4 canonical SMEMs from @lh3's bwa mem poster' +not ok 14 - we can find the right MEMs for a sequence with Ns +# got: 'd41d8cd98f00b204e9800998ecf8427e' +# expected: 'f33b1420b5dc5126f5e74eecc6b79503' +ok 15 - we find the same MEMs sequences with different lengths of Ns +not ok 16 - the GAM index can return the set of alignments mapping to a node +# got: '0' +# expected: '6' +not ok 17 - a subgraph query may be used to obtain a particular subset of alignments from a sorted GAM +# got: '0' +# expected: '15' +not ok 18 - the index can be queried using GAM alignments +# got: '0' +# expected: '1' +not ok 19 - find gets connected edges between queried nodes by default +# got: '0' +# expected: '4' +not ok 20 - find gets nodes provided in a node file list +# got: '0' +# expected: '4' +not ok 21 - extracting by path adds no extra edges +# got: '' +# expected: '1' +ok 22 - pattern based path extraction works +not ok 23 - path DAG range query works +# got: '0' +# expected: '4' +not ok 24 - we can extract a set of targets to separate files +# got: '0' +# expected: '20' +ok 25 - the same extraction can be made using BED input +not ok 26 - we see the expected number of kmers in the given targets +# got: '0' +# expected: '36' +not ok 27 - unnamed test +# got: '1510' +# expected: 'we find the expected number of kmers with haplotype frequency equal to 2' +ok 28 - GFA i/o for find -n consistent with converting both ways +not ok 29 - find nodes that map to the provided node ids +# got: '1' +# expected: '0' +Failed 25/29 subtests +t/06_vg_index.t: line 13: 3284386 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > x.vg +t/06_vg_index.t: line 15: 3284387 Illegal instruction vg index -x x.xg x.vg +t/06_vg_index.t: line 18: 3284388 Illegal instruction vg index -g x.gcsa x.vg +t/06_vg_index.t: line 21: 3284389 Illegal instruction vg index -x x2.xg -g x2.gcsa x.vg +cmp: x.xg: No such file or directory +t/06_vg_index.t: line 27: 3284391 Illegal instruction vg index -g x3.gcsa x.xg +cmp: x.gcsa: No such file or directory +t/06_vg_index.t: line 40: 3284397 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz -a > x.vg +t/06_vg_index.t: line 42: 3284398 Illegal instruction vg index -G x.gbwt -v small/x.vcf.gz x.vg +t/06_vg_index.t: line 45: 3284399 Illegal instruction vg index -x x.xg x.vg +t/06_vg_index.t: line 50: 3284403 Illegal instruction vg index -x x-ap.xg x.vg -L +t/06_vg_index.t: line 55: 3284410 Illegal instruction vg index -g x.gcsa x.vg +t/06_vg_index.t: line 58: 3284411 Illegal instruction vg index -x x2.xg -G x2.gbwt -v small/x.vcf.gz -g x2.gcsa x.vg +cmp: x.xg: No such file or directory +t/06_vg_index.t: line 64: 3284413 Illegal instruction vg index -x x2-ap.xg -G x2-ap.gbwt -v small/x.vcf.gz -g x2-ap.gcsa x.vg -L +cmp: x.gbwt: No such file or directory +t/06_vg_index.t: line 73: 3284421 Illegal instruction vg index -G empty.gbwt -v small/x.vcf.gz --exclude 1 x.vg +t/06_vg_index.t: line 78: 3284423 Illegal instruction vg paths -v x.vg -X -Q _alt > x-alts.gam +t/06_vg_index.t: line 79: 3284424 Illegal instruction vg index x.vg -M x-alts.gam -G x-gam.gbwt +t/06_vg_index.t: line 81: 3284425 Illegal instruction vg convert x.vg -G x-alts.gam > x-alts.gaf +t/06_vg_index.t: line 82: 3284426 Illegal instruction vg index x.vg -F x-alts.gaf -G x-gaf.gbwt +cmp: x-gaf.gbwt: No such file or directory +t/06_vg_index.t: line 95: 3284434 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz -a --region x:100-200 > x.part.vg +t/06_vg_index.t: line 97: 3284435 Illegal instruction vg index -x x.part.xg -G x.part.gbwt --region x:100-200 -v small/x.vcf.gz x.part.vg 2> log.txt +t/06_vg_index.t: line 106: 3284440 Illegal instruction vg construct -r small/xy.fa -v small/xy2.vcf.gz -R x -C > x.vg 2> /dev/null +t/06_vg_index.t: line 107: 3284441 Illegal instruction vg construct -r small/xy.fa -v small/xy2.vcf.gz -R y -C > y.vg 2> /dev/null +t/06_vg_index.t: line 108: 3284442 Illegal instruction vg ids -j x.vg y.vg +t/06_vg_index.t: line 110: 3284443 Illegal instruction vg index -x xy.xg x.vg y.vg +t/06_vg_index.t: line 113: 3284444 Illegal instruction vg index -g xy.gcsa -k 2 x.vg y.vg +t/06_vg_index.t: line 116: 3284445 Illegal instruction vg index -x xy2.xg -g xy2.gcsa -k 2 x.vg y.vg +cmp: xy.xg: No such file or directory +t/06_vg_index.t: line 128: 3284450 Illegal instruction vg construct -r small/xy.fa -v small/xy2.vcf.gz -R x -C -a > x.vg 2> /dev/null +t/06_vg_index.t: line 129: 3284451 Illegal instruction vg construct -r small/xy.fa -v small/xy2.vcf.gz -R y -C -a > y.vg 2> /dev/null +t/06_vg_index.t: line 130: 3284452 Illegal instruction vg ids -j x.vg y.vg +t/06_vg_index.t: line 132: 3284453 Illegal instruction vg index -G x.gbwt -v small/xy2.vcf.gz x.vg +t/06_vg_index.t: line 135: 3284454 Illegal instruction vg index -x xy.xg x.vg y.vg +t/06_vg_index.t: line 138: 3284455 Illegal instruction vg index -g xy.gcsa -k 2 x.vg y.vg +t/06_vg_index.t: line 141: 3284456 Illegal instruction vg index -x xy2.xg -g xy2.gcsa -k 2 x.vg y.vg +t/06_vg_index.t: line 144: 3284457 Illegal instruction vg index -x xy-alt.xg -L x.vg y.vg +t/06_vg_index.t: line 147: 3284458 Illegal instruction vg index -G xy2.gbwt -v small/xy2.vcf.gz xy-alt.xg +cmp: xy.xg: No such file or directory +t/06_vg_index.t: line 161: 3284465 Illegal instruction vg construct -r small/xy.fa -v small/xy2.vcf.gz -R x -C -a > x.vg 2> /dev/null +t/06_vg_index.t: line 163: 3284466 Illegal instruction vg index -G x_ref.gbwt -T x.vg +t/06_vg_index.t: line 173: 3284468 Illegal instruction vg construct -m 1000 -r small/x.fa -v small/x.vcf.gz > x.vg +t/06_vg_index.t: line 174: 3284469 Illegal instruction vg index -x x.xg x.vg bogus123.vg 2> /dev/null +t/06_vg_index.t: line 177: 3284470 Illegal instruction vg kmers -k 16 -gB x.vg > x.graph +t/06_vg_index.t: line 178: 3284471 Illegal instruction vg index -i x.graph -g x.gcsa +t/06_vg_index.t: line 182: 3284473 Illegal instruction vg index -x x.xg -g x.gcsa -k 11 x.vg +t/06_vg_index.t: line 183: 3284475 Illegal instruction vg map -T <(vg sim -n 100 -x x.xg) -d x > x1337.gam +t/06_vg_index.t: line 186: 3284476 Illegal instruction vg gamsort -i x1337.sorted.gam.gai2 x1337.gam > x1337.sorted.gam +t/06_vg_index.t: line 187: 3284477 Illegal instruction vg index --index-sorted-gam x1337.sorted.gam +t/06_vg_index.t: line 189: x1337.sorted.gam.gai: No such file or directory +t/06_vg_index.t: line 189: x1337.sorted.gam.gai2: No such file or directory +t/06_vg_index.t: line 194: 3284483 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > x.vg +t/06_vg_index.t: line 195: 3284484 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > y.vg +t/06_vg_index.t: line 196: 3284485 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > z.vg +t/06_vg_index.t: line 198: 3284486 Illegal instruction vg concat x.vg y.vg z.vg > q.vg +t/06_vg_index.t: line 200: 3284487 Illegal instruction vg index -x q.xg q.vg +t/06_vg_index.t: line 208: 3284490 Illegal instruction vg index -x r.xg reversing/reversing_x.vg +t/06_vg_index.t: line 211: 3284491 Illegal instruction vg index -k 11 -g r.gcsa reversing/reversing_x.vg +t/06_vg_index.t: line 233: 3284525 Illegal instruction vg construct -m 1025 -r 1mb1kgp/z.fa > big.vg +t/06_vg_index.t: line 246: 3284535 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > x.vg +t/06_vg_index.t: line 248: 3284536 Illegal instruction vg snarls -T x.vg > snarls.pb +t/06_vg_index.t: line 251: 3284537 Illegal instruction vg index -j distIndex x.vg +t/06_vg_index.t: line 254: 3284538 Illegal instruction vg convert -v x.vg + 3284539 | vg index -j distIndex - +t/06_vg_index.t: line 257: 3284540 Illegal instruction vg convert -p x.vg + 3284541 | vg index -j distIndex - +t/06_vg_index.t: line 263: 3284543 Illegal instruction vg gbwt -g graph.gbz --gbz-format -G graphs/components_walks.gfa +t/06_vg_index.t: line 264: 3284544 Illegal instruction vg snarls -T graph.gbz > graph.snarls +t/06_vg_index.t: line 265: 3284545 Illegal instruction vg index -j graph.dist graph.gbz +cat: graph.gbz: No such file or directory +t/06_vg_index.t: line 268: 3284546 Exit 1 cat graph.gbz + 3284547 Illegal instruction | vg index -j graph.dist - +t/06_vg_index.t ....... +1..54 +not ok 1 - building an XG index of a graph +# got: '132' +# expected: '0' +not ok 2 - building a GCSA index of a graph +# got: '132' +# expected: '0' +not ok 3 - building both indexes at once +# got: '132' +# expected: '0' +not ok 4 - the indexes are identical when built one at a time and together +# got: '2' +# expected: '0' +not ok 5 - building GCSA from XG +# got: '132' +# expected: '0' +not ok 6 - the GCSA indexes are identical when built from vg and from xg +# got: '2' +# expected: '0' +not ok 7 - building a GBWT index of a graph with haplotypes +# got: '132' +# expected: '0' +not ok 8 - building an XG index of a graph with haplotypes +# got: '132' +# expected: '0' +not ok 9 - xg index does not contain alt paths by default +# got: '0' +# expected: '1' +not ok 10 - building an XG index of a graph with haplotypes and alt paths included +# got: '132' +# expected: '0' +ok 11 - xg index does contains alt paths with index -L +not ok 12 - building a GCSA index of a graph with haplotypes +# got: '132' +# expected: '0' +not ok 13 - building all indexes at once +# got: '132' +# expected: '0' +not ok 14 - the indexes are identical +# got: '2' +# expected: '0' +not ok 15 - building all indexes at once, while leaving alt paths in xg +# got: '132' +# expected: '0' +not ok 16 - the indexes are identical with -L +# got: '2' +# expected: '0' +ok 17 - xg index does contains alt paths with index -L all at once +not ok 18 - samples can be excluded from haplotype indexing +# got: '132' +# expected: '0' +not ok 19 - unnamed test +# got: '0' +# expected: 'excluded samples were not included in the GBWT index' +not ok 20 - GBWT from GAF same as from GAM +# got: '2' +# expected: '0' +not ok 21 - building GBWT index for a regional graph +# got: '132' +# expected: '0' +ok 22 - no warnings about missing variants produced +not ok 23 - building an XG index of multiple graphs +# got: '132' +# expected: '0' +not ok 24 - building a GCSA index of multiple graphs +# got: '132' +# expected: '0' +not ok 25 - building both indexes at once +# got: '132' +# expected: '0' +not ok 26 - the indexes are identical +# got: '2' +# expected: '0' +not ok 27 - building a GBWT index of multiple graphs with haplotypes +# got: '132' +# expected: '0' +not ok 28 - building an XG index of multiple graphs with haplotypes +# got: '132' +# expected: '0' +not ok 29 - building a GCSA index of multiple graphs with haplotypes +# got: '132' +# expected: '0' +not ok 30 - building XG and GCSA indexes at once +# got: '132' +# expected: '0' +not ok 31 - building an XG index with alt paths +# got: '132' +# expected: '0' +not ok 32 - building a GBWT index from an XG index +# got: '132' +# expected: '0' +not ok 33 - the indexes are identical +# got: '2' +# expected: '0' +not ok 34 - GBWT can be built for paths +# got: '132' +# expected: '0' +not ok 35 - fail with nonexistent file +# got: '132' +# expected: '1' +not ok 36 - a prebuilt deBruijn graph in GCSA2 format may be used +# got: '132' +# expected: '0' +ok 37 - vg index and vg gamsort produce identical sorted GAM indexes +not ok 38 - storage of multiple graphs in an index succeeds +# got: '132' +# expected: '0' +not ok 39 - can index backward nodes +# got: '132' +# expected: '0' +not ok 40 - can index kmers for backward nodes +# got: '132' +# expected: '0' +not ok 41 - GCSA2 index works on cyclic graphs with heads and tails +# got: '0' +# expected: '1' +not ok 42 - GCSA2 index works on cyclic graphs with no heads or tails +# got: '0' +# expected: '1' +not ok 43 - GCSA2 index works on cyclic graphs with self loops +# got: '0' +# expected: '1' +not ok 44 - GCSA2 index works on general cyclic graphs +# got: '0' +# expected: '1' +not ok 45 - GCSA2 indexing of a tiny graph works +# got: '0' +# expected: '1' +not ok 46 - GCSA2 indexing succeeds on a single-node graph +# got: '0' +# expected: '1' +not ok 47 - GCSA2 indexing succeeds on graph with heads but no tails +# got: '0' +# expected: '1' +not ok 48 - a useful error message is produced when nodes are too large +# got: '0' +# expected: '1' +not ok 49 - snarl finding with trivial snarls +# got: '132' +# expected: '0' +not ok 50 - building a distance index of a graph +# got: '132' +# expected: '0' +not ok 51 - building a distance index of a piped vg graph +# got: '132' +# expected: '0' +not ok 52 - building a distance index of a piped PackedGraph +# got: '132' +# expected: '0' +not ok 53 - distance index construction from GBZ +# got: '132' +# expected: '0' +not ok 54 - distance index construction from piped GBZ +# got: '132' +# expected: '0' +Failed 50/54 subtests +t/07_vg_map.t: line 10: 3284550 Illegal instruction vg construct -m 1000 -r small/x.fa -v small/x.vcf.gz > x.vg +t/07_vg_map.t: line 11: 3284551 Illegal instruction vg index -x x.xg -g x.gcsa -k 11 x.vg +t/07_vg_map.t: line 35: 3284588 Illegal instruction vg map -s CTACTGACAGCAGAAGTTTGCTGTGAAGATTAAATTAGGTGATGCTTG -d x > /dev/null +printf: usage: printf [-v var] format [arguments] +t/07_vg_map.t: line 56: 3284633 Illegal instruction vg map -d x -f small/r.fa > /dev/null +t/07_vg_map.t: line 62: 3284636 Illegal instruction vg construct -r minigiab/q.fa -v minigiab/NA12878.chr22.tiny.giab.vcf.gz -m 64 > giab.vg +t/07_vg_map.t: line 63: 3284637 Illegal instruction vg index -x giab.xg -g giab.gcsa -k 16 giab.vg +t/07_vg_map.t: line 94: 3284682 Illegal instruction vg paths -d -v cyclic/orient_must_swap_edges.vg > e.vg +t/07_vg_map.t: line 95: 3284683 Illegal instruction vg index -x e.xg -g e.gcsa -k 10 e.vg +t/07_vg_map.t: line 96: 3284684 Illegal instruction vg map -s "ACACCTCCCTCCCGGACGGGGCGGCTGGCC" -d e > /dev/null +t/07_vg_map.t: line 101: 3284686 Illegal instruction vg index -k10 -g g.idx.gcsa -x g.idx.xg graphs/multimap.vg +t/07_vg_map.t: line 106: 3284692 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > x.vg +t/07_vg_map.t: line 107: 3284693 Illegal instruction vg index -x x.xg -g x.gcsa -k 16 x.vg +t/07_vg_map.t: line 112: 3284702 Illegal instruction vg index -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -k 16 graphs/refonly-lrc_kir.vg +t/07_vg_map.t: line 114: 3284703 Illegal instruction vg map -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -i -u 4 -j > temp_paired_alignment.json +t/07_vg_map.t: line 115: 3284704 Illegal instruction vg map -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -u 4 -j > temp_independent_alignment.json +t/07_vg_map.t: line 128: 3284737 Illegal instruction vg map -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -i -j -t 1 --surject-to sam > temp_paired_alignment_xg.sam +t/07_vg_map.t: line 129: 3284738 Illegal instruction vg map -x graphs/refonly-lrc_kir.vg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -i -j -t 1 --surject-to sam > temp_paired_alignment_vg.sam +t/07_vg_map.t: line 141: 3284750 Illegal instruction vg map -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/NONEXISTENT -u 4 -j +t/07_vg_map.t: line 144: 3284751 Illegal instruction vg map -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/NONEXISTENT -i -u 4 -j +t/07_vg_map.t: line 147: 3284752 Illegal instruction vg map -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -f reads/NONEXISTENT -u 4 -j +t/07_vg_map.t: line 150: 3284753 Illegal instruction vg map -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/NONEXISTENT -f reads/grch38_lrc_kir_paired.fq -u 4 -j +t/07_vg_map.t: line 154: 3284754 Illegal instruction vg construct -a -r small/x.fa -v small/x.vcf.gz > x.vg +t/07_vg_map.t: line 155: 3284755 Illegal instruction vg index -x x.xg -g x.gcsa -v small/x.vcf.gz --gbwt-name x.gbwt -k 16 x.vg +t/07_vg_map.t: line 166: 3284769 Illegal instruction vg map -d x -iG <(vg view -a small/x-s13241-n1-p500-v300.gam | sed 's%_1%/1%' | sed 's%_2%/2%' | vg view -JaG -) --surject-to SAM > surjected.sam +t/07_vg_map.t: line 174: 3284805 Illegal instruction vg map -d x -G <(vg view -a small/x-s13241-n1-p500-v300.gam | sed 's%_1%/1%' | sed 's%_2%/2%' | vg view -JaG -) --surject-to SAM > surjected.sam +t/07_vg_map.t: line 183: 3284841 Illegal instruction vg construct -r tiny/tiny.fa -v tiny/tiny.vcf.gz > tiny.vg +t/07_vg_map.t: line 184: 3284842 Illegal instruction vg index -k 16 -x tiny.xg -g tiny.gcsa tiny.vg +t/07_vg_map.t: line 195: 3284853 Illegal instruction vg view -Fv graphs/revdrop.gfa > x.vg +t/07_vg_map.t: line 196: 3284854 Illegal instruction vg index -x x.xg -g x.gcsa x.vg +t/07_vg_map.t ......... +1..55 +not ok 1 - offset counts unused bases from the start of the node on the forward strand +# got: '' +# expected: '3' +not ok 2 - xdrop alignment obtains the expected result +# got: '' +# expected: '3' +not ok 3 - xdrop alignment obtains the expected result for the reverse complement +# got: '' +# expected: '5' +not ok 4 - score-matrix defaults match 1 mismatch -4 should produce same results: with matrixoffset counts unused bases from the start of the node on the forward strand +# got: '' +# expected: '3' +not ok 5 - offset counts unused bases from the start of the node on the reverse strand +# got: '' +# expected: '5' +not ok 6 - global alignment traverses the correct path +# got: '0' +# expected: '4' +not ok 7 - alignment score is as expected +# got: '' +# expected: '58' +not ok 8 - scoring parameters are respected +# got: '' +# expected: '106' +not ok 9 - score-matrix file should give same results as --match 2 --mismatch 2: scoring parameters are respected +# got: '' +# expected: '106' +not ok 10 - full length bonus always be included +# got: '' +# expected: '58' +not ok 11 - full length bonus can be set to 0 +# got: '' +# expected: '96' +not ok 12 - vg map takes -d as input without a variant graph +# got: '132' +# expected: '0' +not ok 13 - vg map can align across a SNP +# got: '0' +# expected: '1' +not ok 14 - alignment works on a small graph +# got: '0' +# expected: '1000' +ok 15 - binary alignment format is equivalent to json version +ok 16 - alignment from BAM correctly handles qualities +not ok 17 - chunky-banded alignment works +# got: '0' +# expected: '1' +not ok 18 - unnamed test +# got: '' +# expected: 'multiple alignments are returned in descending score order' +not ok 19 - only a single primary alignment is returned +# got: '0' +# expected: '1' +not ok 20 - vg can map multi-line FASTA sequences +# got: '132' +# expected: '0' +not ok 21 - mapping of BAM file produces expected number of alignments +# got: '0' +# expected: '3333' +not ok 22 - mapping from a fastq produces the expected number of alignments +# got: '0' +# expected: '3327' +ok 23 - allowing secondary alignments with MEM mapping does not change number of primary alignments +ok 24 - vg connects paired-end reads in gam output +not ok 25 - mapping to graphs that can't be oriented without swapping edges works correctly +# got: '132' +# expected: '0' +not ok 26 - reads multi-map to multiple possible locations +# got: '0' +# expected: '1' +not ok 27 - vg map works based on gcsa and xg indexes +# got: '0' +# expected: '1000' +not ok 28 - unnamed test +# got: '30' +# expected: 'the mapping quality may be capped' +not ok 29 - paired read alignments forced to be consistent have lower score than unrestricted alignments +# got: '0' +# expected: '1' +not ok 30 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments +# got: '0' +# expected: '1' +not ok 31 - only primary alignments have mapping quality scores +# got: '0' +# expected: '2' +not ok 32 - unpaired reads produce mapping quality scores +# got: '0' +# expected: '1000' +ok 33 - map returns same output on xg and vg (single threaded) +not ok 34 - unnamed test +# got: '10' +# expected: 'base quality adjusted alignment produces higher scores if mismatches have low quality' +not ok 35 - error on vg map -f (unpaired) +# got: '132' +# expected: '1' +not ok 36 - error on vg map -f (interleaved) +# got: '132' +# expected: '1' +not ok 37 - error on vg map -f (paired, LHS) +# got: '132' +# expected: '1' +not ok 38 - error on vg map -f (paired, RHS) +# got: '132' +# expected: '1' +not ok 39 - mapping a read that touches unused nodes gets the base score +# got: '' +# expected: '36' +not ok 40 - mapping a read that matches a haplotype gets a small penalty +# got: '' +# expected: '35' +not ok 41 - mapping a read that matches a haplotype with exponent 0 gets the base score +# got: '' +# expected: '36' +not ok 42 - mapping a read that matches no haplotypes gets a larger penalty +# got: '' +# expected: '21' +not ok 43 - surjection of paired reads to SAM yields correct positions +# got: '' +# expected: '321 +# 762' +not ok 44 - surjection of paired reads to SAM yields correct pair partner positions +# got: '' +# expected: '762 +# 321' +not ok 45 - surjection of paired reads to SAM yields properly matched QNAMEs +# got: '0' +# expected: '1' +not ok 46 - surjection of paired reads to SAM produces correct pair partner contigs +# got: '' +# expected: '= +# =' +not ok 47 - surjection of paired reads to SAM produces correct flags +# got: '' +# expected: '163 +# 83' +not ok 48 - surjection of unpaired reads to SAM yields correct positions +# got: '' +# expected: '321 +# 762' +not ok 49 - surjection of unpaired reads to SAM yields correct pair partner positions +# got: '' +# expected: '0 +# 0' +not ok 50 - surjection of unpaired reads to SAM yields distinct QNAMEs +# got: '0' +# expected: '2' +not ok 51 - surjection of unpaired reads to SAM produces absent partner contigs +# got: '' +# expected: '* +# *' +not ok 52 - surjection of unpaired reads to SAM produces correct flags +# got: '' +# expected: '0 +# 16' +not ok 53 - unnamed test +# got: '1' +# expected: 'mapper can read FASTA input' +not ok 54 - unnamed test +# got: '1' +# expected: 'mapper can read multiline FASTA input' +not ok 55 - unnamed test +# got: '130' +# expected: 'xdrop works on a reversed read' +Failed 50/55 subtests +t/08_vg_ids.t: line 16: 3284884 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > x.vg +t/08_vg_ids.t: line 17: 3284885 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > y.vg +t/08_vg_ids.t: line 18: 3284886 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > z.vg +t/08_vg_ids.t: line 20: 3284887 Illegal instruction vg ids -j x.vg y.vg z.vg +(standard_in) 1: syntax error +t/08_vg_ids.t: line 29: 3284904 Illegal instruction vg ids -s cyclic/self_loops.vg > sorted.vg +t/08_vg_ids.t: line 32: 3284905 Illegal instruction vg ids -s cyclic/all.vg > sorted.vg +t/08_vg_ids.t ......... +1..10 +not ok 1 - unnamed test +# got: '1' +# expected: 'minimum node as expected (id compaction correct)' +not ok 2 - unnamed test +# got: '0' +# expected: 'maximum node is as expected (id compaction correct)' +not ok 3 - unnamed test +# got: 'correctly generated joint id space for several graphs' +# expected: '' +not ok 4 - can sort and re-number a graph with self loops +# got: '132' +# expected: '0' +not ok 5 - can sort and renumber a complex cyclic graph +# got: '132' +# expected: '0' +ok 6 - sorting removes back-edges in a DAG +not ok 7 - unnamed test +# got: 'true' +# expected: 'sorting assigns node IDs in topological order' +not ok 8 - unnamed test +# got: 'sorting does not affect id range' +# expected: '' +not ok 9 - unnamed test +# got: 'sorting does not affect id range of vg' +# expected: '' +not ok 10 - unnamed test +# got: 'sorting does not affect id range of hg' +# expected: '' +Failed 9/10 subtests +t/09_vg_concat.t: line 10: 3284940 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > x.vg +t/09_vg_concat.t: line 22: 3284966 Illegal instruction vg view -Jv ./reversing/reversing_path.json > reversing.vg +t/09_vg_concat.t ...... +1..4 +ok 1 - concat doubles the number of nodes +not ok 2 - concat doubles the number of edges + 1 +# got: '0' +# expected: '1' +ok 3 - concat -p doubles the number of nodes on reversing graph +not ok 4 - concat -p doubles the number of edges + 1 on reversing graph +# got: '0' +# expected: '1' +Failed 2/4 subtests +t/100_code_quality.t .. +1..1 +ok 1 - code quality is acceptable +ok +t/10_vg_stats.t: line 10: 3284999 Illegal instruction vg construct -r 1mb1kgp/z.fa -v 1mb1kgp/z.vcf.gz > z.vg +t/10_vg_stats.t: line 33: 3285035 Illegal instruction vg construct -r tiny/tiny.fa -v tiny/tiny.vcf.gz > t.vg +t/10_vg_stats.t: line 38: 3285043 Illegal instruction vg construct -m 1000 -r small/x.fa -a -f -v small/x.vcf.gz > x.vg +t/10_vg_stats.t: line 39: 3285044 Illegal instruction vg index -x x.xg -g x.gcsa -k 16 x.vg +t/10_vg_stats.t: line 40: 3285045 Illegal instruction vg map -x x.xg -g x.gcsa -T small/x-s1337-n100.reads > x.gam +t/10_vg_stats.t: line 48: 3285061 Illegal instruction vg construct -v tiny/tiny.vcf.gz -r tiny/tiny.fa + 3285062 | vg view -g - > tiny_names.gfa +t/10_vg_stats.t: line 51: 3285063 Illegal instruction vg view -Fv tiny_names.gfa > tiny_names.vg +t/10_vg_stats.t: line 56: 3285069 Illegal instruction vg convert graphs/atgc.vg -v > atgc.vg +t/10_vg_stats.t: line 58: 3285071 Illegal instruction vg convert graphs/atgc.vg -a > atgc.hg +t/10_vg_stats.t: line 60: 3285073 Illegal instruction vg convert graphs/atgc.vg -p > atgc.pg +t/10_vg_stats.t: line 62: 3285075 Illegal instruction vg index graphs/atgc.vg -x atgc.xg +t/10_vg_stats.t: line 64: 3285077 Illegal instruction vg convert graphs/atgc.vg -f > atgc.gfa +t/10_vg_stats.t: line 67: 3285080 Illegal instruction vg autoindex -v tiny/tiny.vcf.gz -r tiny/tiny.fa -w giraffe -p tiny +t/10_vg_stats.t: line 79: 3285091 Illegal instruction vg convert -g -a graphs/special_cases.gfa > weird.vg +t/10_vg_stats.t: line 82: 3285092 Illegal instruction vg stats -L weird.vg > loops.txt +cmp: EOF on loops.txt which is empty +t/10_vg_stats.t: line 89: 3285095 Illegal instruction vg stats -e weird.vg > nondeterministic.txt +cmp: EOF on nondeterministic.txt which is empty +t/10_vg_stats.t ....... +1..21 +not ok 1 - unnamed test +# got: '0' +# expected: 'vg stats reports the expected number of nodes' +not ok 2 - unnamed test +# got: '0' +# expected: 'vg stats reports the expected number of edges' +not ok 3 - unnamed test +# got: '0' +# expected: 'vg stats reports the expected graph length' +not ok 4 - vg stats reports the correct number of subgraphs +# got: '0' +# expected: '1' +not ok 5 - unnamed test +# got: 'vg stats reports the correct subgraph length' +# expected: '' +not ok 6 - unnamed test +# got: '38' +# expected: 'distance to head is correct' +not ok 7 - unnamed test +# got: '11' +# expected: 'distance to tail is correct' +not ok 8 - aligned read stats are computed correctly +# got: 'd41d8cd98f00b204e9800998ecf8427e' +# expected: 'd949487d0ea9411b8b2cbffc2ff9a3a0' +ok 9 - basic stats agree between graph formats +not ok 10 - stats can be computed for GAM files without graphs +# got: '' +# expected: 'Total alignments: 100' +not ok 11 - a path overlap description of a test graph has the expected length +# got: '0' +# expected: '113' +not ok 12 - vg stats -F detects format of old protobuf graph +# got: '' +# expected: 'format: VG-Protobuf' +not ok 13 - vg stats -F detects format of newer protobuf graph +# got: '' +# expected: 'format: VG-Protobuf' +not ok 14 - vg stats -F detects format of hash graph +# got: '' +# expected: 'format: HashGraph' +not ok 15 - vg stats -F detects format of packed graph +# got: '' +# expected: 'format: PackedGraph' +not ok 16 - vg stats -F detects format of xg graph +# got: '' +# expected: 'format: XG' +not ok 17 - vg stats -F detects format of GFA graph +# got: '' +# expected: 'format: GFA' +not ok 18 - vg stats -F detects format of GBZ graph +# got: '' +# expected: 'format: GBZ' +0a1 +> 2 12 3 9 8 +not ok 19 - vg stats -D found correct degree distribution of tiny graph +# got: '1' +# expected: '0' +not ok 20 - vg stats -L counts self-loops correctly +# got: '1' +# expected: '0' +not ok 21 - vg stats -e finds the right nondeterministic edge sets +# got: '1' +# expected: '0' +Failed 20/21 subtests +t/11_vg_paths.t: line 12: 3285100 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz -a > x.vg +t/11_vg_paths.t: line 13: 3285101 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > x2.vg +t/11_vg_paths.t: line 14: 3285102 Illegal instruction vg index -x x.xg -G x.gbwt -v small/x.vcf.gz x.vg +t/11_vg_paths.t: line 35: 3285128 Illegal instruction vg paths -x x.xg -Q x -F > x_from_xg.fa +t/11_vg_paths.t: line 38: 3285130 Illegal instruction vg paths -v x.vg -Q x -F > x_from_vg.fa +t/11_vg_paths.t: line 51: 3285163 Illegal instruction vg msga -w 20 -f msgas/q.fa > q.vg +t/11_vg_paths.t: line 57: 3285174 Illegal instruction vg paths -Q s2 -v q.vg -d + 3285175 | vg paths -Ev - > q.len +t/11_vg_paths.t ....... +1..20 +not ok 1 - path listing works from vg +# got: '' +# expected: 'x' +not ok 2 - path listing works from XG +# got: '' +# expected: 'x' +not ok 3 - generic path listing works from XG +# got: '' +# expected: 'x' +not ok 4 - thread listing works from GBWT +# got: '0' +# expected: '2' +not ok 5 - haplotype thread listing works from GBWT +# got: '0' +# expected: '2' +not ok 6 - thread selection by name prefix works correctly +# got: '0' +# expected: '1' +not ok 7 - thread selection by sample name works correctly +# got: '0' +# expected: '2' +ok 8 - no threads are reported for invalid samples +not ok 9 - vg paths may be used to extract threads +# got: '0' +# expected: '2' +not ok 10 - vg paths may be used to extract threads as GAF +# got: '0' +# expected: '2' +0a1,14 +> >x +> CAAATAAGGCTTGGAAATTTTCTGGAGTTCTATTATATTCCAACTCTCTGGTTCCTGGTGCTATGTGTAACTAGTAATGG +> TAATGGATATGTTGGGCTTTTTTCTTTGATTTATTTGAAGTGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAA +> TGGAAAGAATACAAGATTTGGAGCCAGACAAATCTGGGTTCAAATCCTCACTTTGCCACATATTAGCCATGTGACTTTGA +> ACAAGTTAGTTAATCTCTCTGAACTTCAGTTTAATTATCTCTAATATGGAGATGATACTACTGACAGCAGAGGTTTGCTG +> TGAAGATTAAATTAGGTGATGCTTGTAAAGCTCAGGGAATAGTGCCTGGCATAGAGGAAAGCCTCTGACAACTGGTAGTT +> ACTGTTATTTACTATGAATCCTCACCTTCCTTGACTTCTTGAAACATTTGGCTATTGACCTCTTTCCTCCTTGAGGCTCT +> TCTGGCTTTTCATTGTCAACACAGTCAACGCTCAATACAAGGGACATTAGGATTGGCAGTAGCTCAGAGATCTCTCTGCT +> CACCGTGATCTTCAAGTTTGAAAATTGCATCTCAAATCTAAGACCCAGAGGGCTCACCCAGAGTCGAGGCTCAAGGACAG +> CTCTCCTTTGTGTCCAGAGTGTATACGATGTAACTCTGTTCGGGCACTGGTGAAAGATAACAGAGGAAATGCCTGGCTTT +> TTATCAGAACATGTTTCCAAGCTTATCCCTTTTCCCAGCTCTCCTTGTCCCTCCCAAGATCTCTTCACTGGCCTCTTATC +> TTTACTGTTACCAAATCTTTCCAGAAGCTGCTCTTTCCCTCAATTGTTCATTTGTCTTCTTGTCCAGGAATGAACCACTG +> CTCTCTTCTTGTCAGATCAGCTTCTCATCCCTCCTCAAGGGCCTTTAACTACTCCACATCCAAAGCTACCCAGGCCATTT +> TAAGTTTCCTGTGGACTAAGGACAAAGGTGCGGGGAGATGA +not ok 11 - Fasta extracted from xg is the same as the input fasta +# got: '1' +# expected: '0' +0a1,14 +> >x +> CAAATAAGGCTTGGAAATTTTCTGGAGTTCTATTATATTCCAACTCTCTGGTTCCTGGTGCTATGTGTAACTAGTAATGG +> TAATGGATATGTTGGGCTTTTTTCTTTGATTTATTTGAAGTGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAA +> TGGAAAGAATACAAGATTTGGAGCCAGACAAATCTGGGTTCAAATCCTCACTTTGCCACATATTAGCCATGTGACTTTGA +> ACAAGTTAGTTAATCTCTCTGAACTTCAGTTTAATTATCTCTAATATGGAGATGATACTACTGACAGCAGAGGTTTGCTG +> TGAAGATTAAATTAGGTGATGCTTGTAAAGCTCAGGGAATAGTGCCTGGCATAGAGGAAAGCCTCTGACAACTGGTAGTT +> ACTGTTATTTACTATGAATCCTCACCTTCCTTGACTTCTTGAAACATTTGGCTATTGACCTCTTTCCTCCTTGAGGCTCT +> TCTGGCTTTTCATTGTCAACACAGTCAACGCTCAATACAAGGGACATTAGGATTGGCAGTAGCTCAGAGATCTCTCTGCT +> CACCGTGATCTTCAAGTTTGAAAATTGCATCTCAAATCTAAGACCCAGAGGGCTCACCCAGAGTCGAGGCTCAAGGACAG +> CTCTCCTTTGTGTCCAGAGTGTATACGATGTAACTCTGTTCGGGCACTGGTGAAAGATAACAGAGGAAATGCCTGGCTTT +> TTATCAGAACATGTTTCCAAGCTTATCCCTTTTCCCAGCTCTCCTTGTCCCTCCCAAGATCTCTTCACTGGCCTCTTATC +> TTTACTGTTACCAAATCTTTCCAGAAGCTGCTCTTTCCCTCAATTGTTCATTTGTCTTCTTGTCCAGGAATGAACCACTG +> CTCTCTTCTTGTCAGATCAGCTTCTCATCCCTCCTCAAGGGCCTTTAACTACTCCACATCCAAAGCTACCCAGGCCATTT +> TAAGTTTCCTGTGGACTAAGGACAAAGGTGCGGGGAGATGA +not ok 12 - Fasta extracted from vg is the same as the input fasta +# got: '1' +# expected: '0' +not ok 13 - Fasta extracted from threads has correct number of lines +# got: '0' +# expected: '28' +not ok 14 - a single path may be retained +# got: '0' +# expected: '1' +ok 15 - path filtering does not modify the graph +not ok 16 - alt allele paths can be dropped +# got: '0' +# expected: '1' +not ok 17 - unnamed test +# got: '4' +# expected: 'vg path coverage has correct number of columns' +not ok 18 - vg path coverage has correct number of rows +# got: '0' +# expected: '4' +not ok 19 - vg paths found correct number of lengths +# got: '0' +# expected: '2' +ok 20 - vg path coverage reports correct lengths in first column +Failed 17/20 subtests +t/12_vg_kmers.t: line 20: 3285197 Illegal instruction vg construct -v small/x.vcf.gz -r small/x.fa > x.vg +t/12_vg_kmers.t: line 35: 3285215 Illegal instruction vg mod -p -l 11 -e 8 -S jumble/j.vg > j.vg +t/12_vg_kmers.t: line 44: 3285225 Illegal instruction vg construct -v tiny/tiny.vcf.gz -r tiny/tiny.fa + 3285226 | vg view - + 3285227 Done | head -10 + 3285228 | vg view -vF - + 3285229 | vg mod -o - + 3285230 | vg kmers -k 16 - > /dev/null +t/12_vg_kmers.t ....... +1..10 +not ok 1 - correct numbers of kmers in the graph +# got: '0' +# expected: '4250' +not ok 2 - to_end edges are handled correctly +# got: '0' +# expected: '1' +not ok 3 - from_start edges are handled correctly +# got: '0' +# expected: '1' +not ok 4 - GCSA2 output produces the expected number of lines +# got: '0' +# expected: '4356' +not ok 5 - GCSA2 binary output produces the expected number bytes +# got: '0' +# expected: '111528' +not ok 6 - GCSA2 output works when next position is multiple +# got: '' +# expected: 'A,G 7:0,8:0' +not ok 7 - GCSA2 output works when previous characters are multiple +# got: '' +# expected: 'G,A' +not ok 8 - edge-max correctly bounds the number of kmers in a complex graph +# got: '0' +# expected: '26148' +not ok 9 - start/stop node IDs can be specified in GCSA2 output +# got: '0' +# expected: '76' +not ok 10 - attempting to generate kmers longer than the longest path in a graph correctly yields no kmers +# got: '132' +# expected: '0' +Failed 10/10 subtests +t/13_vg_sim.t: line 11: 3285232 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > x.vg +t/13_vg_sim.t: line 12: 3285233 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz -a > x2.vg +t/13_vg_sim.t: line 13: 3285234 Illegal instruction vg index -x x.xg x.vg +t/13_vg_sim.t: line 14: 3285235 Illegal instruction vg index -G x.gbwt -v small/x.vcf.gz x2.vg +t/13_vg_sim.t: line 36: 3285277 Illegal instruction vg sim -n 100 -l 100 -A -x x.xg -r > reads.txt 2> log.txt +t/13_vg_sim.t: line 40: 3285280 Illegal instruction vg sim -n 100 -l 100 -m 1 -g x.gbwt -x x.xg -r > reads.txt 2> log.txt +t/13_vg_sim.t: line 49: 3285288 Illegal instruction vg construct -r n.fa > n.vg +t/13_vg_sim.t: line 50: 3285289 Illegal instruction vg index -x n.xg n.vg +t/13_vg_sim.t: line 59: 3285304 Illegal instruction vg construct -r small/xy.fa -v small/x.vcf.gz -a > xy.vg +t/13_vg_sim.t: line 60: 3285305 Illegal instruction vg index -x xy.xg xy.vg +t/13_vg_sim.t: line 61: 3285306 Illegal instruction vg index -G xy.gbwt -v small/x.vcf.gz xy.vg +t/13_vg_sim.t: line 63: 3285307 Illegal instruction vg sim -s 12345 -n 1000 -l 2 -e 0.1 -x xy.xg -g xy.gbwt --sample-name 1 --any-path > /dev/null +t/13_vg_sim.t: line 74: 3285338 Illegal instruction vg sim -s 12345 -n 1000 -l 2 -e 0.1 -x xy.xg -g xy.gbwt --sample-name 1 --any-path -F minigiab/NA12878.chr22.tiny.fq.gz > /dev/null +t/13_vg_sim.t: line 87: 3285370 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz -a > x.vg +t/13_vg_sim.t: line 88: 3285371 Illegal instruction vg index -x x.xg x.vg +t/13_vg_sim.t: line 94: 3285381 Illegal instruction vg view -Fv graphs/cactus-BRCA2.gfa > cactus-BRCA2.vg +t/13_vg_sim.t: line 95: 3285382 Illegal instruction vg index -x cactus-BRCA2.xg cactus-BRCA2.vg +t/13_vg_sim.t ......... +1..36 +not ok 1 - vg sim creates the correct number of reads +# got: '0' +# expected: '100' +not ok 2 - unnamed test +# got: '110' +# expected: 'end bonuses are included' +not ok 3 - alignments may be generated rather than read sequences +# got: '0' +# expected: '100' +not ok 4 - alignments are produced on both strands +# got: '0' +# expected: '1' +not ok 5 - high simulated error rates do not change the number of bases generated +# got: '0' +# expected: '10300' +ok 6 - vg sim creates forward-strand reads when asked +ok 7 - vg sim can simulate from just a path +ok 8 - vg sim can simulate from just a path in FASTQ mode +not ok 9 - reads can be simulated from all paths +# got: '132' +# expected: '0' +not ok 10 - simulation was successful +# got: '0' +# expected: '1' +not ok 11 - reads can be simulated from GBWT samples +# got: '132' +# expected: '0' +not ok 12 - simulation was successful +# got: '0' +# expected: '1' +not ok 13 - pairs simulated even when fragments overlap +# got: '0' +# expected: '20' +ok 14 - sim does not emit reads with Ns +not ok 15 - sim can emit reads with Ns when asked to +# got: '0' +# expected: '1' +ok 16 - sim doesn't emit Ns even with pair and errors +not ok 17 - Sample simulation works along with --any-path +# got: '132' +# expected: '0' +not ok 18 - not having any regexes skips all unvisited contigs +# got: '0' +# expected: '1000' +not ok 19 - assigning a ploidy of 2 by default gives reads in a ~1-1 ratio vs. diploid covered contigs +# got: '0' +# expected: '1' +not ok 20 - assigning a ploidy of 1 by regex gives reads in a ~1-2 ratio vs. diploid covered contigs +# got: '0' +# expected: '1' +not ok 21 - assigning a ploidy of 0 by regex excludes reads from that contig +# got: '0' +# expected: '1000' +not ok 22 - multiple regexes are interpreted +# got: '0' +# expected: '1000' +not ok 23 - regexes are interpreted as regexes +# got: '0' +# expected: '1000' +not ok 24 - assigning a very high ploidy by regex starves out the other paths +# got: '0' +# expected: '1000' +not ok 25 - Sample simulation works along with --any-path with training FASTQ +# got: '132' +# expected: '0' +not ok 26 - not having any regexes skips all unvisited contigs with training FASTQ +# got: '0' +# expected: '1000' +not ok 27 - assigning a ploidy of 2 by default gives reads in a ~1-1 ratio vs. diploid covered contigs with training FASTQ +# got: '0' +# expected: '1' +not ok 28 - assigning a ploidy of 1 by regex gives reads in a ~1-2 ratio vs. diploid covered contigs with training FASTQ +# got: '0' +# expected: '1' +not ok 29 - assigning a ploidy of 0 by regex excludes reads from that contig with training FASTQ +# got: '0' +# expected: '1000' +not ok 30 - multiple regexes are interpreted with training FASTQ +# got: '0' +# expected: '1000' +not ok 31 - regexes are interpreted as regexes with training FASTQ +# got: '0' +# expected: '1000' +not ok 32 - assigning a very high ploidy by regex starves out the other paths with training FASTQ +# got: '0' +# expected: '1000' +not ok 33 - All reads are annotated with single reference positions by default +# got: '0' +# expected: '1000' +not ok 34 - All reads can be annotated with multiple reference positions when requested +# got: '0' +# expected: '1000' +not ok 35 - ngs trained simulator works +# got: '0' +# expected: '100' +not ok 36 - ngs trained simulator generates gam +# got: '0' +# expected: '200' +Failed 31/36 subtests +t/14_vg_mod.t: line 26: 3285431 Illegal instruction vg mod -n msgas/q_redundant.vg + 3285432 | vg validate - +t/14_vg_mod.t: line 29: 3285433 Illegal instruction vg mod -U 10 msgas/q_redundant.vg + 3285434 | vg validate - +t/14_vg_mod.t: line 32: 3285435 Illegal instruction vg mod -u msgas/q_redundant.vg + 3285436 | vg validate - +t/14_vg_mod.t: line 46: 3285465 Illegal instruction vg view -Jv reversing/reversing_path.json + 3285466 | vg mod -X 3 - + 3285467 | vg validate - +t/14_vg_mod.t: line 58: 3285487 Illegal instruction vg msga -w 20 -f msgas/s.fa > s.vg +t/14_vg_mod.t: line 59: 3285488 Illegal instruction vg msga -g s.vg -s TCAGATTCTCATCCCTCCTCAAGGGCTTCTGTAGCTTTGATGTGGAGTAGTTCCAGGCCATTTTAAGTTTCCTGTGGACTAAGGACAAAGGTGCGGGGAG -w 16 -N > s2.vg +t/14_vg_mod.t: line 60: 3285489 Illegal instruction vg mod -u s2.vg > /dev/null +t/14_vg_mod.t: line 64: 3285491 Illegal instruction vg msga -f msgas/l.fa -b a1 -w 16 + 3285492 | vg mod -X 8 - + 3285493 | vg validate - +t/14_vg_mod.t: line 67: 3285494 Illegal instruction vg mod -U 3 graphs/atgclinv2.vg + 3285495 | vg validate - +t/14_vg_mod.t: line 70: 3285496 Illegal instruction vg mod -U 3 graphs/atgclinv2.vg + 3285497 | vg mod -f 50 - + 3285498 | vg validate - +t/14_vg_mod.t: line 77: 3285555 Illegal instruction vg mod -f 6 graphs/atgclinv2.vg + 3285556 | vg mod -d 5 - + 3285557 | vg validate - +t/14_vg_mod.t: line 84: 3285596 Illegal instruction vg mod -w 100 graphs/ununrollable.vg + 3285597 | vg validate - +t/14_vg_mod.t: line 87: 3285598 Illegal instruction vg mod -s graphs/not-simple.vg + 3285599 | vg validate - +t/14_vg_mod.t: line 90: 3285600 Illegal instruction vg msga -g <(vg msga -f msgas/cycle.fa -b s1 -w 19 -O 18 -k 4 -t 1 | vg paths -d -v - | vg mod -U 10 -) -f msgas/cycle.fa -t 1 + 3285601 | vg mod -N - + 3285602 | vg paths -d -v - + 3285604 | vg mod -U 10 - > c.vg +t/14_vg_mod.t: line 96: 3285618 Illegal instruction vg construct -r small/x.fa -a -f -v small/x.vcf.gz > x.vg +t/14_vg_mod.t: line 97: 3285619 Illegal instruction vg mod -v small/x.vcf.gz x.vg > x.sample.vg +t/14_vg_mod.t ......... +1..32 +ok 1 - vg mod yields a graph with only a particular path +not ok 2 - orphan edge removal is automatic +# got: '0' +# expected: '8' +not ok 3 - unnamed test +# got: '285' +# expected: 'graph complexity reduction works as expected' +not ok 4 - unnamed test +# got: '983' +# expected: 'short subgraph pruning works' +not ok 5 - normalization produces the correct number of nodes +# got: '0' +# expected: '4' +not ok 6 - normalization removes redundant SNP alleles +# got: '0' +# expected: '4' +not ok 7 - normalization produces a valid graph +# got: '132' +# expected: '0' +not ok 8 - looped normalization produces a valid graph +# got: '132' +# expected: '0' +not ok 9 - unchop produces a valid graph +# got: '132' +# expected: '0' +not ok 10 - unnamed test +# got: '154' +# expected: 'normalization removes redundant sequence in the graph' +not ok 11 - normalization doesn't introduce cycles and does remove redundancy in bubbles +# got: 'd41d8cd98f00b204e9800998ecf8427e' +# expected: '3233892f7cb5a387561e064f2545ebee' +ok 12 - vg mod removes non-path nodes and edge +not ok 13 - chopping a graph works correctly with reverse mappings +# got: '132' +# expected: '0' +not ok 14 - unnamed test +# got: '2f785068c91dbe84177c1fd679b6f133' +# expected: 'unchop correctly handles paths' +ok 15 - unchop correctly handles a graph with an inversion +not ok 16 - unchop handles doubly-reversing edges +# got: '' +# expected: '1' +ok 17 - normalization works on a graph with an inversion +not ok 18 - mod successfully unchops a difficult graph +# got: '132' +# expected: '0' +not ok 19 - chopping self-cycling nodes retains the cycle +# got: '132' +# expected: '0' +not ok 20 - unrolling works and produces a valid graph +# got: '132' +# expected: '0' +not ok 21 - unfolding works and produces a valid graph +# got: '132' +# expected: '0' +ok 22 - dagify-unroll produces a graph with the same kmers as the original graph +ok 23 - unfold produces a graph with the same kmers as the original graph +not ok 24 - dagify handles a graph with two strongly connected components +# got: '132' +# expected: '0' +not ok 25 - unnamed test +# got: '0' +# expected: 'unfold followed by dagify produces a graph with no cycles' +ok 26 - unfold followed by dagify produces a graph with the same kmers as the original graph +not ok 27 - dagify unrolls the un-unrollable graph +# got: '132' +# expected: '0' +not ok 28 - sibling simplification does not disrupt paths +# got: '132' +# expected: '0' +not ok 29 - unnamed test +# got: '4' +# expected: 'dagify correctly calculates the minimum distance through the unrolled component' +not ok 30 - unnamed test +# got: '200' +# expected: 'dagify produces a graph of the correct size' +not ok 31 - subsetting a flat-alleles graph to a sample graph works +# got: '' +# expected: '1041' +not ok 32 - removal of high-degree nodes results in the expected number of subgraphs +# got: '0' +# expected: '7' +Failed 25/32 subtests +t/15_vg_surject.t: line 11: 3285629 Illegal instruction vg construct -r small/x.fa > j.vg +t/15_vg_surject.t: line 12: 3285630 Illegal instruction vg index -x j.xg j.vg +t/15_vg_surject.t: line 13: 3285631 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > x.vg +t/15_vg_surject.t: line 14: 3285632 Illegal instruction vg index -k 11 -g x.gcsa -x x.xg x.vg +t/15_vg_surject.t: line 17: 3285633 Illegal instruction vg map -G small/x-allref-nohptrouble.gam -g x.gcsa -x x.xg > j.gam +t/15_vg_surject.t: line 19: 3285637 Illegal instruction vg map -G <(vg sim -a -n 100 -x x.xg) -g x.gcsa -x x.xg > x.gam +t/15_vg_surject.t: line 42: 3285670 Illegal instruction vg paths -X -x x.vg + 3285671 | vg view -aj - + 3285672 Done | jq '.name = "sample#0#x#0"' + 3285673 | vg view -JGa - > paths.gam +t/15_vg_surject.t: line 43: 3285674 Illegal instruction vg paths -X -x x.vg + 3285675 | vg view -aj - + 3285676 Done | jq '.name = "ref#0#x[55]"' + 3285677 | vg view -JGa - >> paths.gam +t/15_vg_surject.t: line 44: 3285678 Illegal instruction vg augment x.vg -i paths.gam > x.aug.vg +t/15_vg_surject.t: line 45: 3285679 Illegal instruction vg index -x x.aug.xg x.aug.vg +rm: cannot remove 'x.aug.xg': No such file or directory +[main_samview] fail to read the header from "-". +t/15_vg_surject.t: line 84: 3285728 Illegal instruction vg map -f fwd.fq -g x.gcsa -x x.xg > mapped.fwd.gam +t/15_vg_surject.t: line 85: 3285729 Illegal instruction vg map -f rev.fq -g x.gcsa -x x.xg > mapped.rev.gam +[main_samview] fail to read the header from "-". +t/15_vg_surject.t: line 99: 3285756 Done echo '{"sequence": "CAAATAA", "path": {"mapping": [{"position": {"node_id": 1}, "edit": [{"from_length": 7, "to_length": 7}]}]}, "mapping_quality": 99}' + 3285757 Illegal instruction | vg view -JGa - > read.gam +t/15_vg_surject.t: line 102: 3285762 Done echo '{"name": "read/2", "sequence": "CAAATAA", "path": {"mapping": [{"position": {"node_id": 1}, "edit": [{"from_length": 7, "to_length": 7}]}]}, "fragment_prev": {"name": "read/1"}}{"name": "read/1", "sequence": "CTTATTT", "path": {"mapping": [{"position": {"node_id": 1, "is_reverse": true}, "edit": [{"from_length": 7, "to_length": 7}]}]}, "fragment_next": {"name": "read/2"}}' + 3285763 Illegal instruction | vg view -JGa - > read.gam +t/15_vg_surject.t: line 105: 3285768 Illegal instruction vg surject -p x -x x.xg -i read.gam -s > read.gam.surject.sam +t/15_vg_surject.t: line 106: 3285769 Illegal instruction vg convert x.xg -G read.gam -t 1 + 3285770 | vg surject -p x -x x.xg -i -G - -s > read.gaf.surject.sam +t/15_vg_surject.t: line 111: 3285773 Illegal instruction vg map -d x -iG <(vg view -a small/x-s13241-n1-p500-v300.gam | sed 's%_1%/1%' | sed 's%_2%/2%' | vg view -JaG -) + 3285774 | vg surject -x x.xg -p x -s -i -N Sample1 -R RG1 - > surjected.sam +t/15_vg_surject.t: line 122: 3285822 Illegal instruction vg mod -c graphs/fail.vg > f.vg +t/15_vg_surject.t: line 123: 3285823 Illegal instruction vg index -k 11 -g f.gcsa -x f.xg f.vg +t/15_vg_surject.t: line 131: 3285830 Illegal instruction vg mod -c graphs/fail2.vg > f.vg +t/15_vg_surject.t: line 132: 3285831 Illegal instruction vg index -k 11 -g f.gcsa -x f.xg f.vg +t/15_vg_surject.t: line 139: 3285838 Illegal instruction vg construct -r minigiab/q.fa -v minigiab/NA12878.chr22.tiny.giab.vcf.gz > minigiab.vg +t/15_vg_surject.t: line 140: 3285839 Illegal instruction vg index -k 11 -g m.gcsa -x m.xg minigiab.vg +[main_samview] fail to read the header from "-". +[main_samview] fail to read the header from "-". +t/15_vg_surject.t: line 151: 3285873 Illegal instruction vg construct -r small/x.fa > j.vg +t/15_vg_surject.t: line 152: 3285874 Illegal instruction vg index j.vg -g j.gcsa +t/15_vg_surject.t: line 153: 3285875 Illegal instruction vg map -x j.vg -g j.gcsa -s TGGAAAGAATACAAGATTTGGAGCCAGACAAATCTGGGTTCAAATCCTCACTTTGCCACATATTAGCCATGTGACTTTGA > r.gam +t/15_vg_surject.t: line 154: 3285876 Illegal instruction vg surject -x j.vg r.gam -s > r.sam +t/15_vg_surject.t: line 157: 3285879 Illegal instruction vg construct -r x.sub.fa > j.sub.vg +t/15_vg_surject.t: line 158: 3285880 Illegal instruction vg index j.sub.vg -g j.sub.gcsa +t/15_vg_surject.t: line 159: 3285881 Illegal instruction vg map -x j.sub.vg -g j.sub.gcsa -s TGGAAAGAATACAAGATTTGGAGCCAGACAAATCTGGGTTCAAATCCTCACTTTGCCACATATTAGCCATGTGACTTTGA > r.sub.gam +t/15_vg_surject.t: line 160: 3285882 Illegal instruction vg surject -x j.sub.vg r.sub.gam -s > r.sub.sam +t/15_vg_surject.t: line 168: 3285887 Illegal instruction vg surject -x j.sub.vg r.sub.gam -s --ref-paths path_info.tsv > r.sub.sam +t/15_vg_surject.t: line 175: 3285892 Illegal instruction vg surject -s -x surject/perpendicular.vg surject/perpendicular.gam > perpendicular.sam +t/15_vg_surject.t: line 179: 3285897 Illegal instruction vg surject -s --prune-low-cplx -x surject/perpendicular.vg surject/perpendicular.gam > perpendicular.sam +t/15_vg_surject.t: line 185: 3285903 Illegal instruction vg construct -r small/x.fa > x.vg +t/15_vg_surject.t: line 186: 3285904 Done cat <(vg view x.vg) <(vg view x.vg | grep P | sed 's/P\tx/P\ty/') + 3285905 Illegal instruction | vg convert -g - > x.pathdup.vg +t/15_vg_surject.t: line 187: 3285911 Illegal instruction vg index -x x.xg -g x.gcsa x.pathdup.vg +t/15_vg_surject.t: line 188: 3285912 Illegal instruction vg sim -x x.xg -n 20 -l 40 -p 60 -v 10 -a > x.gam +t/15_vg_surject.t: line 189: 3285913 Illegal instruction vg mpmap -x x.xg -g x.gcsa -n dna --suppress-mismapping -B -G x.gam -i -F GAM -I 60 -D 10 > mapped.gam +t/15_vg_surject.t: line 190: 3285914 Illegal instruction vg mpmap -x x.xg -g x.gcsa -n dna --suppress-mismapping -B -G x.gam -i -F GAMP -I 60 -D 10 > mapped.gamp +rm: cannot remove 'x.xg': No such file or directory +rm: cannot remove 'x.gcsa': No such file or directory +rm: cannot remove 'x.gcsa.lcp': No such file or directory +t/15_vg_surject.t ..... +1..47 +not ok 1 - reads are generated +# got: '0' +# expected: '100' +not ok 2 - vg surject works perfectly for perfect reads without misaligned homopolymer indels derived from the reference +# got: '0' +# expected: '100' +not ok 3 - vg surject works perfectly for perfect reads without misaligned homopolymer indels derived from the reference +# got: '0' +# expected: '100' +not ok 4 - vg surject actually places reads on the correct path +# got: '0' +# expected: '100' +not ok 5 - vg surject doesn't need to be told which path to use +# got: '0' +# expected: '100' +not ok 6 - vg surject reports alignment scores +# got: '0' +# expected: '100' +not ok 7 - vg surject picks a reference-sense path if it is present +# got: '0' +# expected: '100' +not ok 8 - vg surject works for every read simulated from a dense graph +# got: '0' +# expected: '100' +not ok 9 - vg surject spliced algorithm works for every read simulated from a dense graph +# got: '0' +# expected: '100' +not ok 10 - vg surject produces valid SAM output +# got: '0' +# expected: '100' +not ok 11 - vg map may surject reads to produce valid SAM output +# got: '0' +# expected: '100' +not ok 12 - vg map may surject reads to produce valid BAM output +# got: '0' +# expected: '100' +not ok 13 - vg surject retains read names +# got: '0' +# expected: '100' +not ok 14 - vg surject can set sample and read group +# got: '0' +# expected: '100' +not ok 15 - we respect the original mapping's softclips +# got: '0' +# expected: '1' +ok 16 - quality strings we will use for testing are oriented correctly +ok 17 - forward and reverse orientations of a read produce the same surjected SAM, ignoring flags +not ok 18 - vg surject produces valid BAM output +# got: '0' +# expected: '100' +not ok 19 - mapping quality is preserved through surjection +# got: '' +# expected: '99' +not ok 20 - read pairing is preserved through GAM->GAM surjection +# got: '' +# expected: 'read/1' +ok 21 - interleaved surjection produces same SAM when using GAF and GAM inputs +not ok 22 - surjection of paired reads to SAM yields correct positions +# got: '' +# expected: '321 +# 762' +not ok 23 - surjection of paired reads to SAM yields correct pair partner positions +# got: '' +# expected: '762 +# 321' +not ok 24 - surjection of paired reads to SAM yields properly matched QNAMEs +# got: '0' +# expected: '1' +not ok 25 - surjection of paired reads to SAM produces correct pair partner contigs +# got: '' +# expected: '= +# =' +not ok 26 - surjection of paired reads to SAM produces correct flags +# got: '' +# expected: '83 +# 163' +not ok 27 - surjection of paired reads to SAM tags both reads with a read group +# got: '0' +# expected: '2' +not ok 28 - surjection of paired reads to SAM creates RG header +# got: '0' +# expected: '1' +not ok 29 - surjection works for a longer (151bp) read +# got: '0' +# expected: '1' +not ok 30 - surjection works for another difficult read +# got: '0' +# expected: '1' +not ok 31 - mapping reproduces qualities from BAM input +# got: '0' +# expected: '1' +not ok 32 - mapping reproduces qualities from fastq input +# got: '0' +# expected: '1' +not ok 33 - mapping reproduces qualities from GAF input +# got: '0' +# expected: '1' +not ok 34 - surject works on GAMP input +# got: '0' +# expected: '1000' +not ok 35 - surject works on paired GAMP input +# got: '0' +# expected: '1000' +ok 36 - vg surject correctly handles subpath suffix in path name +ok 37 - vg surject correctly fetches base path length from input file +not ok 38 - vg surject does not crash when surjecting a read that grazes the reference with a deletion +# got: '132' +# expected: '0' +not ok 39 - vg surject leaves a read that grazes the reference with a deletion unmapped +# got: '' +# expected: '4' +not ok 40 - vg surject does not crash when surjecting a read that grazes the reference with a deletion and pruning low complexity anchors +# got: '132' +# expected: '0' +not ok 41 - vg surject leaves a read that grazes the reference with a deletion unmapped when pruning low complexity anchors +# got: '' +# expected: '4' +not ok 42 - GAM surject can return only primaries +# got: '0' +# expected: '40' +not ok 43 - GAM surject can return multimappings +# got: '0' +# expected: '80' +not ok 44 - GAM surject can return paired multimappings +# got: '0' +# expected: '80' +not ok 45 - GAMP surject can return only primaries +# got: '0' +# expected: '40' +not ok 46 - GAMP surject can return multimappings +# got: '0' +# expected: '80' +not ok 47 - GAMP surject can return multimappings +# got: '0' +# expected: '80' +Dubious, test returned 1 (wstat 256, 0x100) +Failed 42/47 subtests +t/16_vg_msga.t: line 24: 3285961 Illegal instruction vg msga -f msgas/s.fa -w 16 + 3285962 | vg mod -U 10 - + 3285963 | vg mod -c - + 3285964 | vg view -j - +t/16_vg_msga.t: line 28: 3285965 Illegal instruction vg construct -v tiny/tiny.vcf.gz -r tiny/tiny.fa > t.vg +t/16_vg_msga.t: line 34: 3285995 Illegal instruction vg msga -f msgas/s.fa -b s1 -w 20 -O 10 + 3285996 | vg mod -U 10 - + 3285997 | vg mod -c - > s.vg +t/16_vg_msga.t: line 35: 3285998 Illegal instruction vg msga -g s.vg -f msgas/s-rev.fa -w 20 -O 10 + 3285999 | vg mod -U 10 - + 3286000 | vg mod -c - > s+rev.vg +t/16_vg_msga.t: line 41: 3286025 Illegal instruction vg msga -f msgas/w.fa -b x -K 16 -w 20 + 3286026 | vg validate - +t/16_vg_msga.t: line 44: 3286027 Illegal instruction vg msga -f GRCh38_alts/FASTA/HLA/K-3138.fa -w 256 -W 64 -E 4 + 3286028 | vg validate - +t/16_vg_msga.t: line 47: 3286029 Illegal instruction vg msga -f msgas/cycle.fa -b s1 -w 64 -t 1 + 3286030 | vg validate - +t/16_vg_msga.t: line 52: 3286037 Illegal instruction vg msga -f msgas/l.fa -b a1 -w 16 + 3286038 | vg validate - +t/16_vg_msga.t: line 55: 3286039 Illegal instruction vg msga -f GRCh38_alts/FASTA/HLA/B-3106.fa -w 256 -E 4 -B 4 -W 64 -P 0.9 + 3286040 | vg validate - +t/16_vg_msga.t: line 58: 3286041 Illegal instruction vg msga -f msgas/inv.fa -w 16 -O 5 + 3286042 | vg validate - +t/16_vg_msga.t ........ +1..14 +not ok 1 - MSGA produces the expected graph for GRCh38 HLA-V +# got: 'd41d8cd98f00b204e9800998ecf8427e' +# expected: '16e56f0090b310d2b1479d49cf790324' +not ok 2 - X-drop DP MSGA produces the expected graph for GRCh38 HLA-V +# got: 'd41d8cd98f00b204e9800998ecf8427e' +# expected: '2ab075dd73c31ea9939726d72c12655f' +not ok 3 - soft clips at node boundaries (start) are included correctly +# got: '0' +# expected: '1' +not ok 4 - soft clips at node boundaries (end) are included correctly +# got: '0' +# expected: '1' +ok 5 - region hints (-p) produce same graph +ok 6 - adding in existing sequences in reverse doesn't change graph +not ok 7 - the paths of the graph encode the original sequences used to build it +# got: '0' +# expected: '2' +not ok 8 - even when banding the paths of the graph encode the original sequences used to build it +# got: '132' +# expected: '0' +not ok 9 - HLA K-3138 correctly includes all input paths +# got: '132' +# expected: '0' +not ok 10 - a difficult cyclic path can be included to produce a valid graph +# got: '132' +# expected: '0' +not ok 11 - a reference sequence set representing an inversion in it may be msga'd and detected +# got: '0' +# expected: '1' +not ok 12 - edges in cycles with two nodes are correctly included +# got: '132' +# expected: '0' +not ok 13 - HLA B-3106 is assembled into a valid graph +# got: '132' +# expected: '0' +not ok 14 - odd-sized overlaps may be used for chunked alignment +# got: '132' +# expected: '0' +Failed 12/14 subtests +t/17_vg_augment.t: line 11: 3286044 Illegal instruction vg view -J -v pileup/tiny.json > tiny.vg +t/17_vg_augment.t: line 14: 3286045 Illegal instruction vg view -J -a -G pileup/edits.json > edits.gam +t/17_vg_augment.t: line 15: 3286046 Illegal instruction vg augment -a direct tiny.vg edits.gam -A edits-embedded.gam > augmented.vg +t/17_vg_augment.t: line 22: 3286053 Illegal instruction vg augment -a direct tiny.vg edits.gam -A edits-embedded.gam -m 1 > augmented.m1.vg +t/17_vg_augment.t: line 26: 3286055 Illegal instruction vg convert tiny.vg -G edits.gam > edits.gaf +t/17_vg_augment.t: line 27: 3286056 Illegal instruction vg augment -a direct tiny.vg edits.gaf -F -A edits-embedded.gaf > augmented.gaf.vg +t/17_vg_augment.t: line 28: 3286057 Illegal instruction vg convert augmented.gaf.vg -F edits-embedded.gaf > edits-embedded.gaf.gam +t/17_vg_augment.t: line 35: 3286065 Illegal instruction vg view -J -a -G pileup/edit.json > edit.gam +t/17_vg_augment.t: line 36: 3286066 Illegal instruction vg augment -a direct tiny.vg edit.gam -A edit-embedded.gam > augmented.vg +t/17_vg_augment.t: line 48: 3286075 Illegal instruction vg construct -m 1000 -r tiny/tiny.fa > t.vg +t/17_vg_augment.t: line 49: 3286076 Illegal instruction vg index -k 11 -g t.idx.gcsa -x t.idx.xg t.vg +t/17_vg_augment.t: line 69: 3286123 Illegal instruction vg construct -v tiny/tiny.vcf.gz -r tiny/tiny.fa > t.vg +t/17_vg_augment.t: line 70: 3286124 Illegal instruction vg align -s GGGGGGGAAATTTTCTGGAGTTCTATTATATTCCAAAAAAAAAA t.vg > t.gam +Usage: grep [OPTION]... PATTERNS [FILE]... +Try 'grep --help' for more information. +Usage: grep [OPTION]... PATTERNS [FILE]... +Try 'grep --help' for more information. +t/17_vg_augment.t: line 73: 3286145 Illegal instruction vg align -s AAATTTTCTGGAGTTCTAT t.vg >> t.gam +t/17_vg_augment.t: line 74: 3286146 Illegal instruction vg find -x t.vg -n 9 -c 1 > n9.vg +t/17_vg_augment.t: line 75: 3286147 Illegal instruction vg augment n9.vg t.gam -s -A n9_aug.gam > /dev/null +t/17_vg_augment.t: line 79: 3286152 Illegal instruction vg construct -m 1000 -r small/x.fa -v small/x.vcf.gz > x.vg +t/17_vg_augment.t: line 80: 3286153 Illegal instruction vg index -x x.xg -g x.gcsa -k 16 x.vg +t/17_vg_augment.t: line 81: 3286154 Illegal instruction vg map -x x.xg -g x.gcsa -G small/x-s1337-n100-e0.01-i0.005.gam -t 1 > x.gam +t/17_vg_augment.t: line 82: 3286155 Illegal instruction vg augment -Z x.trans -i -S x.vg x.gam > x.mod.vg +t/17_vg_augment.t: line 86: 3286160 Illegal instruction vg construct -m 1000 -r tiny/tiny.fa > flat.vg +t/17_vg_augment.t: line 87: 3286161 Illegal instruction vg view flat.vg + 3286162 Done | sed 's/CAAATAAGGCTTGGAAATTTTCTGGAGTTCTATTATATTCCAACTCTCTG/CAAATAAGGCTTGGAAATTTTCTGGAGATCTATTATACTCCAACTCTCTG/' + 3286163 | vg view -Fv - > 2snp.vg +t/17_vg_augment.t: line 88: 3286164 Illegal instruction vg index -x 2snp.xg 2snp.vg +t/17_vg_augment.t: line 89: 3286165 Illegal instruction vg sim -s 2323 -l 30 -x 2snp.xg -n 30 -a > 2snp.sim +t/17_vg_augment.t: line 90: 3286166 Illegal instruction vg index -x flat.xg -g flat.gcsa -k 16 flat.vg +t/17_vg_augment.t: line 91: 3286167 Illegal instruction vg map -g flat.gcsa -x flat.xg -G 2snp.sim -k 8 > 2snp.gam +t/17_vg_augment.t: line 94: 3286175 Illegal instruction vg view flat.vg + 3286176 Done | sed 's/CAAATAAGGCTTGGAAATTTTCTGGAGTTCTATTATATTCCAACTCTCTG/CAAATAAGGCTTGGAAATTATCTGGAGTTCTATTATATCCCAACTCTCTG/' + 3286177 | vg view -Fv - > 2err.vg +t/17_vg_augment.t: line 95: 3286178 Illegal instruction vg sim -s 2323 -l 30 -x 2err.vg -n 10 -a > 2err.sim +t/17_vg_augment.t: line 96: 3286179 Illegal instruction vg map -g flat.gcsa -x flat.xg -G 2err.sim -k 8 > 2err.gam +t/17_vg_augment.t: line 116: 3286198 Illegal instruction vg map -g flat.gcsa -x flat.xg -f qual.fq -k 8 > 2qual.gam +t/17_vg_augment.t: line 123: 3286214 Illegal instruction vg convert flat.vg -p > flat.pg +t/17_vg_augment.t: line 127: 3286222 Illegal instruction vg convert flat.vg -a > flat.hg +t/17_vg_augment.t: line 135: 3286232 Illegal instruction vg construct -m 10 -r tiny/tiny.fa > t.vg +t/17_vg_augment.t: line 136: 3286233 Illegal instruction vg index -k 11 -g t.idx.gcsa -x t.idx.xg t.vg +t/17_vg_augment.t: line 140: 3286243 Illegal instruction vg map -s CAAATAAGGCTTGGAAATTTGGNGGTCTGGAGTTCTATTATATTCCAACTCTCTG -d t.idx + 3286244 | vg augment t.vg - -N 1 -m 0 > t.aug1.vg +t/17_vg_augment.t: line 145: 3286250 Illegal instruction vg map -s CAAATAAGGCTTGGAAATTTGGNGGTCTGGAGTTCTATTATATTCCAACTCTCTG -d t.idx + 3286251 | vg augment t.vg - -N 0.5 -m 1 > t.aug1f.vg +t/17_vg_augment.t: line 150: 3286257 Illegal instruction vg map -s CAAATAAGGCTTGGAAATTTGGNGGTCTGGAGTTCTATTATATTCCAACTCTCTG -d t.idx + 3286258 | vg augment t.vg - -N 0.1 > t.aug1nf.vg +t/17_vg_augment.t: line 157: 3286265 Illegal instruction vg map -s CAGAGAGTTGGAATATAATAGAACTCCAGACCNCCAAATTTCCAAGCCTTATTTG -d t.idx + 3286266 | vg augment t.vg - -N 1 -m 0 > t.augr1.vg +t/17_vg_augment.t: line 162: 3286272 Illegal instruction vg map -s CAGAGAGTTGGAATATAATAGAACTCCAGACCNCCAAATTTCCAAGCCTTATTTG -d t.idx + 3286273 | vg augment t.vg - -N 0.5 -m 1 > t.augr1f.vg +t/17_vg_augment.t: line 167: 3286279 Illegal instruction vg map -s CAGAGAGTTGGAATATAATAGAACTCCAGACCNCCAAATTTCCAAGCCTTATTTG -d t.idx + 3286280 | vg augment t.vg - -N 0.1 > t.augr1nf.vg +t/17_vg_augment.t: line 174: 3286287 Illegal instruction vg map -s CAAATAAGGCTTGGAGGNGGAATTTTCTGGAGTTCTATTATATTCCAACTCTCTG -d t.idx + 3286288 | vg augment t.vg - -N 1 -m 0 > t.aug1.vg +t/17_vg_augment.t: line 177: 3286295 Illegal instruction vg map -s CAAATAAGGCTTGGAGGNGGAATTTTCTGGAGTTCTATTATATTCCAACTCTCTG -d t.idx + 3286296 | vg augment t.vg - -N 0.5 -m 1 > t.aug1.vg +t/17_vg_augment.t: line 180: 3286303 Illegal instruction vg map -s CAAATAAGGCTTGGAGGNGGAATTTTCTGGAGTTCTATTATATTCCAACTCTCTG -d t.idx + 3286304 | vg augment t.vg - -N 0.1 > t.aug1.vg +t/17_vg_augment.t: line 185: 3286312 Illegal instruction vg map -s CAGAGAGTTGGAATATAATAGAACTCCAGAAAATTCCNCCTCCAAGCCTTATTTG -d t.idx + 3286313 | vg augment t.vg - -N 1 -m 0 > t.aug1.vg +t/17_vg_augment.t: line 188: 3286320 Illegal instruction vg map -s CAGAGAGTTGGAATATAATAGAACTCCAGAAAATTCCNCCTCCAAGCCTTATTTG -d t.idx + 3286321 | vg augment t.vg - -N 0.5 -m 1 > t.aug1.vg +t/17_vg_augment.t: line 191: 3286328 Illegal instruction vg map -s CAGAGAGTTGGAATATAATAGAACTCCAGAAAATTCCNCCTCCAAGCCTTATTTG -d t.idx + 3286329 | vg augment t.vg - -N 0.1 > t.aug1.vg +t/17_vg_augment.t: line 196: 3286337 Illegal instruction vg map -s CAAATANNNAGGCTTGGAAATTTTCTGGAGTTCTATTATATNNNNNTCCAACTCTCTG -d t.idx > t.gam +t/17_vg_augment.t: line 197: 3286338 Illegal instruction vg augment t.vg t.gam -N 0.5 -A t.aug1.gam > t.aug1.vg +t/17_vg_augment.t: line 202: 3286345 Illegal instruction vg map -s CAGAGAGTTGGANNNNNATATAATAGAACTCCAGAAAATTTCCAAGCCTNNNTATTTG -d t.idx > t.gam +t/17_vg_augment.t: line 203: 3286346 Illegal instruction vg augment t.vg t.gam -N 0.5 -A t.aug1.gam > t.aug1.vg +t/17_vg_augment.t ..... +1..39 +not ok 1 - direct augmentation embeds reads fully for well-supported SNPs +# got: '0' +# expected: '36' +not ok 2 - adding a well-supported SNP by direct augmentation adds 3 more nodes +# got: '' +# expected: '18' +not ok 3 - adding a well-supported SNP by direct augmentation adds 3 more nodes with -m 1 +# got: '' +# expected: '18' +not ok 4 - direct augmentation embeds with GAF reads fully for well-supported SNPs +# got: '0' +# expected: '36' +not ok 5 - adding a well-supported SNP by direct augmentation with GAF adds 3 more nodes +# got: '' +# expected: '18' +not ok 6 - direct augmentation embeds reads fully for probable errors +# got: '0' +# expected: '3' +not ok 7 - adding a probable error by direct augmentation adds 3 more nodes +# got: '' +# expected: '18' +not ok 8 - path inclusion does not modify the graph when alignment is a perfect match +# got: '0' +# expected: '1' +not ok 9 - path inclusion does not modify the graph when alignment has a SNP but doesnt meet the coverage threshold +# got: '0' +# expected: '1' +not ok 10 - unnamed test +# got: '1+' +# expected: 'path inclusion does not modify the included path when alignment has a SNP but doesnt meet the coverage threshold' +not ok 11 - output GAM has single edit when SNP was filtered out due to coverage +# got: '0' +# expected: '1' +not ok 12 - path inclusion with a complex variant introduces the right number of nodes +# got: '0' +# expected: '5' +not ok 13 - path inclusion works for deletions +# got: '0' +# expected: '1' +not ok 14 - SNPs can be included in the graph +# got: '0' +# expected: '4' +not ok 15 - unnamed test +# got: 'GGGGG' +# expected: 'a soft clip at read start becomes a new head of the graph' +not ok 16 - unnamed test +# got: 'AAAAAAAA' +# expected: 'a soft clip at read end becomes a new tail of the graph' +not ok 17 - augment -s works as desired +# got: '0' +# expected: '1' +not ok 18 - the expected graph translation is exported when the graph is edited +# got: '0' +# expected: '1290' +not ok 19 - editing the graph with many SNP-containing alignments does not introduce duplicate identical nodes +# got: '0' +# expected: '7' +ok 20 - augmenting 2 snps with -m 1 produces the same nodes as default +ok 21 - augmenting 2 snps and 2 errors with -m 11 produces the same nodes as with just the snps +not ok 22 - augmenting with 2snps makes correct number of nodes +# got: '0' +# expected: '7' +not ok 23 - low-quality snp is filtered +# got: '0' +# expected: '4' +ok 24 - augmenting a packed graph produces same results as a vg graph +ok 25 - augmenting a hash graph produces same results as a vg graph +0a1 +> GGNGG +not ok 26 - augmenting between nodes without filters works as expected +# got: '1' +# expected: '0' +0a1 +> GGNGG +not ok 27 - augmenting between nodes with inactive filters works as expected +# got: '1' +# expected: '0' +ok 28 - augmenting between nodes N filter works as expected +0a1 +> GGNGG +not ok 29 - augmenting between nodes without filters works as expected on reverse strand +# got: '1' +# expected: '0' +0a1 +> GGNGG +not ok 30 - augmenting between nodes with inactive filters works as expected on reverse strand +# got: '1' +# expected: '0' +ok 31 - augmenting between nodes N filter works as expected on reverse strand +not ok 32 - augmenting within node without filters works as expected +# got: '0' +# expected: '1' +not ok 33 - augmenting within node with inactive filters works as expected +# got: '0' +# expected: '1' +ok 34 - augmenting within node with N filter works as expected +not ok 35 - augmenting within node without filters works as expected on reverse strand +# got: '0' +# expected: '1' +not ok 36 - augmenting within node with inactive filters works as expected on reverse strand +# got: '0' +# expected: '1' +ok 37 - augmenting within node with N filter works as expected on reverse strand +not ok 38 - unnamed test +# got: 'CAAATAAGGCTTGGAAATTTTCTGGAGTTCTATTATATTCCAACTCTCTG' +# expected: 'sequence in filtered alignment has removed insertion' +not ok 39 - unnamed test +# got: 'CAGAGAGTTGGAATATAATAGAACTCCAGAAAATTTCCAAGCCTTATTTG' +# expected: 'sequence in filtered alignment has removed insertion on reverse strand' +Failed 31/39 subtests +t/18_vg_call.t: line 13: 3286354 Illegal instruction vg view -J -v call/tiny.json > tiny.vg +t/18_vg_call.t: line 17: 3286355 Illegal instruction vg augment tiny.vg empty.gam -A empty_aug.gam > tiny_aug.vg +t/18_vg_call.t: line 18: 3286356 Illegal instruction vg index tiny_aug.vg -x tiny_aug.xg +t/18_vg_call.t: line 19: 3286357 Illegal instruction vg pack -x tiny_aug.xg -g empty_aug.gam -o tiny_aug.pack +t/18_vg_call.t: line 20: 3286358 Illegal instruction vg call tiny_aug.xg -k tiny_aug.pack > tiny_aug.vcf +t/18_vg_call.t: line 26: 3286363 Illegal instruction vg construct -r inverting/miniFasta.fa -v inverting/miniFasta_VCFinversion.vcf.gz -S > miniFastaGraph.vg +t/18_vg_call.t: line 27: 3286364 Illegal instruction vg index -x miniFastaGraph.xg -g miniFastaGraph.gcsa miniFastaGraph.vg +t/18_vg_call.t: line 28: 3286365 Illegal instruction vg sim -x miniFastaGraph.xg -n 1000 -l 30 -a -s 1 > miniFasta.gam +t/18_vg_call.t: line 29: 3286366 Illegal instruction vg map -G miniFasta.gam -g miniFastaGraph.gcsa -x miniFastaGraph.xg > miniFastaGraph.gam +t/18_vg_call.t: line 30: 3286367 Illegal instruction vg augment miniFastaGraph.vg miniFastaGraph.gam -A mappedminitest_aug.gam > mappedminitest_aug.vg +t/18_vg_call.t: line 31: 3286368 Illegal instruction vg index mappedminitest_aug.vg -x mappedminitest_aug.xg +t/18_vg_call.t: line 32: 3286369 Illegal instruction vg pack -x mappedminitest_aug.xg -g mappedminitest_aug.gam -o mappedminitest_aug.pack +t/18_vg_call.t: line 33: 3286370 Illegal instruction vg call mappedminitest_aug.xg -k mappedminitest_aug.pack > calledminitest.vcf +t/18_vg_call.t: line 40: 3286376 Illegal instruction vg construct -r inverting/miniFasta.fa -v inverting/miniFasta_VCFinversion.vcf.gz -S > miniFastaGraph.vg +t/18_vg_call.t: line 41: 3286377 Illegal instruction vg index -x miniFastaGraph.xg -g miniFastaGraph.gcsa miniFastaGraph.vg +t/18_vg_call.t: line 42: 3286378 Illegal instruction vg sim -x miniFastaGraph.xg -n 1000 -l 30 -a -s 1 > miniFasta.gam +t/18_vg_call.t: line 43: 3286379 Illegal instruction vg construct -r inverting/miniFasta.fa > miniFastaFlat.vg +t/18_vg_call.t: line 44: 3286380 Illegal instruction vg sim -x miniFastaFlat.vg -n 500 -l 30 -a -s 1 >> miniFasta.gam +t/18_vg_call.t: line 45: 3286381 Illegal instruction vg map -G miniFasta.gam -g miniFastaGraph.gcsa -x miniFastaGraph.xg > miniFastaGraph.gam +t/18_vg_call.t: line 46: 3286382 Illegal instruction vg augment miniFastaGraph.vg miniFastaGraph.gam -A mappedminitest_aug.gam > mappedminitest_aug.vg +t/18_vg_call.t: line 47: 3286383 Illegal instruction vg index mappedminitest_aug.vg -x mappedminitest_aug.xg +t/18_vg_call.t: line 48: 3286384 Illegal instruction vg pack -x mappedminitest_aug.xg -g mappedminitest_aug.gam -o mappedminitest_aug.pack +t/18_vg_call.t: line 49: 3286385 Illegal instruction vg call mappedminitest_aug.xg -k mappedminitest_aug.pack -d 1 > calledminitest.vcf +t/18_vg_call.t: line 58: 3286391 Illegal instruction vg augment -i call/HGSVC_chr22_17119590_17880307.vg call/HGSVC_chr22_17119590_17880307_alts.gam > HGSVC_alts.vg +t/18_vg_call.t: line 60: 3286392 Illegal instruction vg index HGSVC_alts.vg -x HGSVC_alts.xg -L +t/18_vg_call.t: line 62: 3286393 Illegal instruction vg pack -x HGSVC_alts.xg -g call/HGSVC_chr22_17119590_17880307.gam -o HGSVC_alts.pack +t/18_vg_call.t: line 64: 3286394 Illegal instruction vg call HGSVC_alts.xg -k HGSVC_alts.pack -v call/HGSVC_chr22_17200000_17800000.vcf.gz -s HG00514 > HGSVC.vcf +t/18_vg_call.t: line 74: 3286412 Illegal instruction vg call HGSVC_alts.xg -k HGSVC_alts.pack -v call/HGSVC_chr22_17200000_17800000.vcf.gz -s HG00514 -d 1 > HGSVC1.vcf +t/18_vg_call.t: line 84: 3286431 Illegal instruction vg call HGSVC_alts.xg -k HGSVC_alts.pack -s HG00514 -a > HGSVC2.vcf +t/18_vg_call.t: line 92: 3286440 Illegal instruction vg index HGSVC_alts.xg -F HGSVC_travs.gaf.gz -G HGSVC_travs.gbwt +t/18_vg_call.t: line 93: 3286441 Illegal instruction vg call HGSVC_alts.xg -k HGSVC_alts.pack -g HGSVC_travs.gbwt -s HG00514 > HGSVC_travs.vcf +t/18_vg_call.t: line 94: 3286442 Illegal instruction vg call HGSVC_alts.xg -k HGSVC_alts.pack -s HG00514 > HGSVC_direct.vcf +t/18_vg_call.t: line 111: 3286469 Illegal instruction vg construct -a -r small/x.fa -v small/x.vcf.gz > x.vg +t/18_vg_call.t: line 112: 3286470 Illegal instruction vg index -x x.xg x.vg -L +t/18_vg_call.t: line 113: 3286471 Illegal instruction vg sim -s 1 -n 1000 -l 150 -x x.xg -a > sim.gam +t/18_vg_call.t: line 114: 3286472 Illegal instruction vg pack -x x.xg -g sim.gam -o x.xg.cx +t/18_vg_call.t: line 115: 3286473 Illegal instruction vg pack -x x.vg -g sim.gam -o x.vg.cx +t/18_vg_call.t: line 116: 3286474 Illegal instruction vg snarls x.xg > x.snarls +t/18_vg_call.t: line 117: 3286475 Illegal instruction vg call x.xg -k x.xg.cx -r x.snarls -t 1 > x.xg.vcf +t/18_vg_call.t: line 118: 3286476 Illegal instruction vg call x.vg -k x.vg.cx -r x.snarls -t 1 > x.vg.vcf +t/18_vg_call.t: line 122: 3286478 Illegal instruction vg call x.xg -k x.xg.cx -r x.snarls -t 1 -v tiny/tiny.vcf.gz > x.xg.gt.vcf +t/18_vg_call.t: line 123: 3286479 Illegal instruction vg call x.vg -k x.vg.cx -r x.snarls -t 1 -v tiny/tiny.vcf.gz > x.vg.gt.vcf +t/18_vg_call.t: line 130: 3286482 Illegal instruction vg msga -f msgas/cycle.fa -b s1 -w 64 -t 1 > c.vg +t/18_vg_call.t: line 131: 3286483 Illegal instruction vg index -x c.xg -g c.gcsa c.vg +t/18_vg_call.t: line 137: 3286486 Illegal instruction vg construct -r m.fa > m.vg +t/18_vg_call.t: line 138: 3286487 Illegal instruction vg index -x m.xg m.vg +t/18_vg_call.t: line 139: 3286488 Illegal instruction vg sim -n 200 -s 23823 -l 50 -x m.xg -a > m.sim +t/18_vg_call.t: line 140: 3286489 Illegal instruction vg map -x c.xg -g c.gcsa -G m.sim > m.gam +t/18_vg_call.t: line 141: 3286490 Illegal instruction vg augment c.vg m.gam -A m.aug.gam > c.aug.vg +t/18_vg_call.t: line 142: 3286491 Illegal instruction vg index -x c.aug.xg c.aug.vg +t/18_vg_call.t: line 143: 3286492 Illegal instruction vg pack -x c.aug.xg -g m.aug.gam -o m.aug.pack +t/18_vg_call.t: line 144: 3286493 Illegal instruction vg call c.aug.xg -k m.aug.pack > m.vcf +t/18_vg_call.t: line 149: 3286500 Illegal instruction vg autoindex -r small/x.fa -v small/x.vcf.gz -w giraffe -p x +mv: cannot stat 'x.giraffe.gbz': No such file or directory +t/18_vg_call.t: line 152: 3286503 Illegal instruction vg gbwt -Z x.gbz -o x.gbwt -g x.gg +t/18_vg_call.t: line 153: 3286504 Illegal instruction vg convert x.gg -b x.gbwt -p > x.vg +t/18_vg_call.t: line 155: 3286505 Illegal instruction vg sim -x x.vg -P 1#0#x#0 -n 500 -a -s 23 > sim.gam +t/18_vg_call.t: line 156: 3286506 Illegal instruction vg sim -x x.vg -P 1#1#x#0 -n 500 -a -s 23 >> sim.gam +t/18_vg_call.t: line 158: 3286507 Illegal instruction vg pack -x x.vg -o x.pack -g sim.gam +t/18_vg_call.t: line 159: 3286508 Illegal instruction vg call x.vg -k x.pack -a > call.vcf +t/18_vg_call.t: line 160: 3286509 Illegal instruction vg call x.vg -k x.pack -g x.gbwt > callg.vcf +t/18_vg_call.t: line 163: 3286518 Illegal instruction vg call x.gbz -k x.pack -z > callz.vcf +t/18_vg_call.t: line 177: 3286537 Illegal instruction vg construct -r x_sub1.fa -v x_sub1.vcf.gz -r x_sub2.fa -v x_sub2.vcf.gz > x_subs.vg +t/18_vg_call.t: line 178: 3286538 Illegal instruction vg sim -x x_subs.vg -n 1000 -a -s 23 > sim.gam +t/18_vg_call.t: line 179: 3286539 Illegal instruction vg pack -x x_subs.vg -o x_subs.pack -g sim.gam +t/18_vg_call.t: line 180: 3286540 Illegal instruction vg call x_subs.vg -k x_subs.pack > x_subs.vcf +t/18_vg_call.t: line 184: 3286554 Illegal instruction vg call x_subs.vg -k x_subs.pack -p x -l 50000 > x_subs_override.vcf +t/18_vg_call.t ........ +1..19 +ok 1 - calling empty gam gives empty VCF +not ok 2 - Called microinversion +# got: '0' +# expected: '1' +ok 3 - Called no microinversion with haploid setting +ok 4 - Fewer than 8 differences between called and true SV genotypes +ok 5 - Fewer than 8 differences between called haploid and truncated true SV genotypes +ok 6 - Same number of reference calls with -a as with -v +ok 7 - Calling from extracted traversals by way of GBWT produces same genotypes as calling directly +ok 8 - Fewer than 3 differences between allales called via traversals or directly +ok 9 - call output same on vg as xg +ok 10 - call output same on vg as xg +not ok 11 - vg call finds true homozygous variants in a cyclic graph +# got: '0' +# expected: '3' +ok 12 - vg call finds same variants when using gbwt to enumerate traversals +ok 13 - call produces same output with gbwt and gbz +not ok 14 - vg call makes currect base path header with subpath input +# got: '0' +# expected: '1' +not ok 15 - vg call makes only currect base path header with subpath input +# got: '0' +# expected: '1' +ok 16 - vg call only reports base paths with subpath input +not ok 17 - vg call makes currect base path header with subpath input and override +# got: '0' +# expected: '1' +not ok 18 - vg call makes only currect base path header with subpath input and override +# got: '0' +# expected: '1' +ok 19 - overriding contig length does not change calls +Failed 6/19 subtests +t/19_vg_compare.t ..... skipped: (no reason given) +rapper: Parsing file with parser turtle and base URI http://example.org/vg +rapper: Parsing returned 0 triples +rapper: Parsing file with parser turtle and base URI http://example.org/vg +rapper: Parsing returned 0 triples +t/20_vgtordf.t ........ +1..6 +not ok 1 - vg view produces the expected number of lines of turtle +# got: '0' +# expected: '90' +not ok 2 - vg view produces the expected number of lines of turtle +# got: '0' +# expected: '90' +ok 3 - rapper passed +ok 4 - rapper passed +not ok 5 - vg view produces the expected number of lines of turtle +# got: '0' +# expected: '5' +not ok 6 - vg view produces the expected number of lines of turtle +# got: '0' +# expected: '5' +Failed 4/6 subtests +t/21_vg_filter.t: line 10: 3286594 Illegal instruction vg construct -m 1000 -r small/x.fa -v small/x.vcf.gz > x.vg +t/21_vg_filter.t: line 11: 3286595 Illegal instruction vg index -x x.xg x.vg +t/21_vg_filter.t: line 12: 3286596 Illegal instruction vg sim -x x.xg -l 100 -n 5000 -e 0.01 -i 0.001 -a > x.gam +t/21_vg_filter.t: line 49: 3286614 Illegal instruction vg surject -x x.xg -s -i paired.gam > paired.sam +[main_samview] fail to read the header from "paired.sam". +t/21_vg_filter.t: line 49: 3286623 Illegal instruction vg surject -x x.xg -s single.gam > single.sam +[main_samview] fail to read the header from "single.sam". +t/21_vg_filter.t: line 51: 3286632 Illegal instruction vg filter -d 123.5 -t 10 paired.gam > filtered.gam +t/21_vg_filter.t: line 56: 3286640 Illegal instruction vg filter -d 0.2 -t 10 single.gam > filtered.gam +t/21_vg_filter.t: line 60: 3286647 Illegal instruction vg annotate -p -x x.xg -a paired.gam > paired.annotated.gam +t/21_vg_filter.t: line 68: 3286672 Illegal instruction vg index -x g.xg -g g.gcsa -k 16 graphs/refonly-lrc_kir.vg +t/21_vg_filter.t: line 69: 3286673 Illegal instruction vg mpmap -x g.xg -g g.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -I 10 -D 50 -F GAM -t 1 > g.proper.gam +t/21_vg_filter.t: line 70: 3286674 Illegal instruction 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 > g.improper.gam +rm: cannot remove 'g.xg': No such file or directory +rm: cannot remove 'g.gcsa': No such file or directory +rm: cannot remove 'g.gcsa.lcp': No such file or directory +t/21_vg_filter.t ...... +1..13 +not ok 1 - vg filter with no options preserves input. +# got: '0' +# expected: '5000' +not ok 2 - vg filter downsamples correctly +# got: '1' +# expected: '0' +ok 3 - samtools 1.0+ and vg filter agree on how to select downsampled paired reads +ok 4 - samtools 1.0+ and vg filter agree on how to select downsampled unpaired reads +not ok 5 - reads with refpos annotations not matching an exclusion regex are let through +# got: '0' +# expected: '200' +ok 6 - reads with refpos annotations matching an exclusion regex are removed +ok 7 - negating a non-filter results in no reads +ok 8 - a filter and its complement should form the entire file +not ok 9 - properly paired read passes proper filter +# got: '0' +# expected: '2' +ok 10 - improperly paired read fails proper filter +ok 11 - read pairs can be tropped by feature +not ok 12 - read pairs can be kept if only one read fails +# got: '0' +# expected: '2' +ok 13 - unmapped reads can be filtered out +Failed 5/13 subtests +t/22_ggsv.t ........... skipped: (no reason given) +t/23_vectorize.t ...... skipped: (no reason given) +t/25_circularize.t: line 10: 3286707 Illegal instruction vg construct -r tiny/tiny.fa -v tiny/tiny.vcf.gz + 3286708 | vg circularize -p x - > circular.vg +t/25_circularize.t: line 14: 3286713 Illegal instruction vg index -x circular.xg circular.vg +t/25_circularize.t: line 15: 3286714 Illegal instruction vg convert circular.xg -v > extracted.vg +t/25_circularize.t .... +1..2 +not ok 1 - a path may be circularized +# got: '0' +# expected: '1' +not ok 2 - a circular path survives a round trip to/from xg +# got: '0' +# expected: '1' +Failed 2/2 subtests +t/26_deconstruct.t: line 10: 3286721 Illegal instruction vg msga -f GRCh38_alts/FASTA/HLA/V-352962.fa -t 1 -k 16 + 3286722 | vg mod -U 10 - + 3286723 | vg mod -c - > hla.vg +t/26_deconstruct.t: line 11: 3286724 Illegal instruction vg index hla.vg -x hla.xg +t/26_deconstruct.t: line 13: 3286725 Illegal instruction vg deconstruct hla.xg -p "gi|157734152:29563108-29564082" > hla_decon.vcf +t/26_deconstruct.t: line 16: 3286733 Illegal instruction vg deconstruct hla.xg -p "gi|568815592:29791752-29792749" > hla_decon.vcf +t/26_deconstruct.t: line 20: 3286741 Illegal instruction vg deconstruct hla.xg -p "gi|568815592:29791752-29792749" -e > hla_decon_path.vcf +t/26_deconstruct.t: line 40: 3286774 Illegal instruction vg view -Fv inv.gfa > inv.vg +t/26_deconstruct.t: line 41: 3286775 Illegal instruction vg index inv.vg -x inv.xg +t/26_deconstruct.t: line 42: 3286776 Illegal instruction vg deconstruct inv.xg -p x -e > inv_decon.vcf +t/26_deconstruct.t: line 50: 3286781 Illegal instruction vg deconstruct inv.xg -p y -e > inv_decon.vcf +t/26_deconstruct.t: line 56: 3286785 Illegal instruction vg gbwt -G inv.gfa -g inv.chop.gbz --gbz-format --max-node 5 +t/26_deconstruct.t: line 57: 3286786 Illegal instruction vg deconstruct inv.chop.gbz -p x -O > inv.chop.decon +t/26_deconstruct.t: line 58: 3286787 Illegal instruction vg gbwt -G inv.gfa -g inv.gbz --gbz-format --max-node 1025 +t/26_deconstruct.t: line 59: 3286788 Illegal instruction vg deconstruct inv.gbz -p x -O > inv.decon +t/26_deconstruct.t: line 66: 3286791 Illegal instruction vg construct -v small/x.vcf.gz -r small/x.fa + 3286792 | vg view -g - > cyclic_small.gfa +t/26_deconstruct.t: line 69: 3286793 Illegal instruction vg view -Fv cyclic_small.gfa > cyclic_small.vg +t/26_deconstruct.t: line 70: 3286794 Illegal instruction vg index cyclic_small.vg -x cyclic_small.xg +t/26_deconstruct.t: line 71: 3286795 Illegal instruction vg deconstruct cyclic_small.xg -p y -e > cyclic_small_decon.vcf +t/26_deconstruct.t: line 79: 3286800 Illegal instruction vg deconstruct cyclic_small.xg -p x -e > cyclic_small_decon.vcf +t/26_deconstruct.t: line 87: 3286805 Illegal instruction vg construct -v tiny/tiny.vcf.gz -r tiny/tiny.fa + 3286806 | vg view -g - > cyclic_tiny.gfa +t/26_deconstruct.t: line 90: 3286807 Illegal instruction vg view -Fv cyclic_tiny.gfa > cyclic_tiny.vg +t/26_deconstruct.t: line 91: 3286808 Illegal instruction vg index cyclic_tiny.vg -x cyclic_tiny.xg +t/26_deconstruct.t: line 92: 3286809 Illegal instruction vg find -x cyclic_tiny.xg -n 10 -n 11 -n 12 -n 13 -n 14 -n 15 -c 1 > cycle.vg +t/26_deconstruct.t: line 93: 3286810 Illegal instruction vg index cycle.vg -x cycle.xg +t/26_deconstruct.t: line 94: 3286811 Illegal instruction vg deconstruct cycle.xg -p y -e -t 1 > cycle_decon.vcf +t/26_deconstruct.t: line 105: 3286824 Illegal instruction vg construct -v tiny/tiny.vcf.gz -r tiny/tiny.fa + 3286825 | vg view -g - > tiny_names.gfa +t/26_deconstruct.t: line 111: 3286826 Illegal instruction vg view -Fv tiny_names.gfa > tiny_names.vg +t/26_deconstruct.t: line 112: 3286827 Illegal instruction vg index tiny_names.vg -x tiny_names.xg +t/26_deconstruct.t: line 123: 3286847 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz -a > x.vg +t/26_deconstruct.t: line 124: 3286848 Illegal instruction vg index -x x.xg -G x.gbwt -v small/x.vcf.gz x.vg +t/26_deconstruct.t: line 127: bcftools: command not found +t/26_deconstruct.t: line 128: bcftools: command not found +t/26_deconstruct.t: line 129: bcftools: command not found +t/26_deconstruct.t: line 130: bcftools: command not found +t/26_deconstruct.t: line 136: 3286862 Illegal instruction vg autoindex -r small/x.fa -v small/x.vcf.gz -w giraffe -p x +t/26_deconstruct.t: line 137: 3286863 Illegal instruction vg deconstruct x.giraffe.gbz > x.gbz.decon.vcf +t/26_deconstruct.t: line 146: 3286867 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz + 3286868 | vg view - > small_cluster.gfa +t/26_deconstruct.t: line 150: 3286869 Illegal instruction vg deconstruct small_cluster.gfa -p x > small_cluster_0.vcf +t/26_deconstruct.t: line 151: 3286870 Illegal instruction vg deconstruct small_cluster.gfa -p x -L 0.3 > small_cluster_3.vcf +t/26_deconstruct.t: line 158: 3286881 Illegal instruction vg deconstruct nesting/nested_snp_in_del.gfa -p x -nR > nested_snp_in_del.vcf +t/26_deconstruct.t: line 169: 3286889 Illegal instruction vg deconstruct nesting/nested_snp_in_del.gfa -p x -n > nested_snp_in_del.vcf +t/26_deconstruct.t: line 178: 3286894 Illegal instruction vg deconstruct nesting/nested_snp_in_ins.gfa -p x -n > nested_snp_in_ins.vcf +t/26_deconstruct.t: line 207: 3286916 Illegal instruction vg snarls nesting/nested_snp_in_nested_ins.gfa -A cactus > nested_snp_in_nested_ins.snarls +t/26_deconstruct.t: line 208: 3286917 Illegal instruction vg deconstruct nesting/nested_snp_in_nested_ins.gfa -r nested_snp_in_nested_ins.snarls -P x -n > nested_snp_in_nested_ins.vcf +t/26_deconstruct.t: line 215: 3286931 Illegal instruction vg deconstruct nesting/nested_snp_in_ins_cycle.gfa -P x -n > nested_snp_in_ins_cycle.vcf +t/26_deconstruct.t .... +1..37 +not ok 1 - deconstructed hla vcf has correct number of sites +# got: '0' +# expected: '17' +not ok 2 - unnamed test +# got: 'C-CGCGGGCGCCGTGGATGGAGCA' +# expected: 'deconstructed hla vcf has correct insertion' +not ok 3 - deconstructed hla vcf with other path has correct number of sites +# got: '0' +# expected: '17' +not ok 4 - unnamed test +# got: 'CGCGGGCGCCGTGGATGGAGCA-C' +# expected: 'deconstructed hla vcf has correct deletion' +ok 5 - path-based and exhaustive decontruction give equivalent sites when expected +not ok 6 - unnamed test +# got: '1' +# expected: 'path that differs from reference in every alt has correct genotype' +not ok 7 - unnamed test +# got: '0' +# expected: 'path that is same as reference in every alt has correct genotype' +not ok 8 - unnamed test +# got: '##contig=' +# expected: 'reference contig correctly written' +0a1 +> x 10 CTTGGAAATTTTCTGGAGTT AACTCCAGAAAATTTCCAAG 1 +not ok 9 - deconstruct correctly handles a simple inversion +# got: '1' +# expected: '0' +0a1 +> y 10 AACTCCAGAAAATTTCCAAG CTTGGAAATTTTCTGGAGTT 1 +not ok 10 - deconstruct correctly handles a simple inversion when the reference contains the reversing edge +# got: '1' +# expected: '0' +ok 11 - deconstruct applies translation from gbz with -O +0a1 +> y 121 TGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAACGTTTGACAATCTATCACCAGGGGTAATGTGGGGAAA TGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAA 1 +not ok 12 - deconstruct correctly handles a cycle in the reference path when contained inside snarl +# got: '1' +# expected: '0' +0a1 +> x 121 TGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAA TGACGTTTGACAATCTATCACTAGGGGTAATGTGGGGAAACGTTTGACAATCTATCACCAGGGGTAATGTGGGGAAA 1 +not ok 13 - deconstruct correctly handles a cycle in the alt path +# got: '1' +# expected: '0' +not ok 14 - cyclic reference deconstruction has correct number of variants +# got: '0' +# expected: '1' +0a1 +> y 44 A T 1 +not ok 15 - deconstruct correctly handles cycle in the reference path that spans snarl +# got: '1' +# expected: '0' +not ok 16 - -P -H options return correct number of variants +# got: '0' +# expected: '2' +not ok 17 - -P -H options use correct reference name +# got: '0' +# expected: '2' +ok 18 - -P -H does not find conflict in alt1 in second variant +ok 19 - deconstructing vg graph gives same output as xg graph +ok 20 - haplotype 1 preserved when deconstructing small test with gbwt +ok 21 - haplotype 2 preserved when deconstructing small test with gbwt +ok 22 - gbz deconstruction gives same output as gbwt deconstruction +not ok 23 - cluster-free deconstruction finds all alt alleles +# got: '' +# expected: 'GATTTGA,G' +not ok 24 - clustered deconstruction finds fewer alt alleles +# got: '' +# expected: 'G' +not ok 25 - clustered deconstruction finds correct allele info +# got: '' +# expected: '0:0.333:0' +0a1,2 +> CATG CAAG,C 1|2 +> T A,* 1|2 +not ok 26 - nested deconstruction gets correct star-allele for snp inside deletion +# got: '1' +# expected: '0' +not ok 27 - PA=0 correctly set at both sites of neseted deletion +# got: '0' +# expected: '2' +0a1,2 +> CATG CAAG,C 1|2 +> T A 1|. +not ok 28 - nested deconstruction gets correct allele for snp inside deletion (without -R) +# got: '1' +# expected: '0' +0a1,2 +> A T 0|1 +> C CAAG,CATG 1|2 +not ok 29 - nested deconstruction gets correct allele for snp inside insert +# got: '1' +# expected: '0' +not ok 30 - PA=0 set for base allele of nested insertion +# got: '0' +# expected: '1' +not ok 31 - PA=1 set for nested allele of nested insertion +# got: '0' +# expected: '1' +0a1,2 +> ##contig= +> ##contig= +not ok 32 - nested deconstruction gets correct contigs in vcf header for snp inside insert +# got: '1' +# expected: '0' +0a1,2 +> A T,* 0|1 0|2 +> C CAAG,CATG 1|2 1|0 +not ok 33 - nested deconstruction gets correct star allele for snp ins2.ide ins2.ert +# got: '1' +# expected: '0' +not ok 34 - unnamed test +# got: 'AC=1,1;AF=0.5,0.5;AN=2;AT=>1>6,>1>2>3>31>33>34>35>5>6,>1>2>3>31>32>34>35>5>6;NS=1;PA=0;PL=1;PR=1;RC=x;RD=1;RL=1;RS=1;LV=0' +# expected: 'INFO tags correct for level-0 site of double-nested SNP' +not ok 35 - unnamed test +# got: 'AC=1;AF=0.5;AN=2;AT=>2>3>31>33>34>35>5,>2>3>31>32>34>35>5;NS=1;PA=1;PL=8;PR=1;RC=x;RD=1;RL=8;RS=1;LV=1;PS=>1>6' +# expected: 'INFO tags correct for level-1 site of double-nested SNP' +not ok 36 - unnamed test +# got: 'AC=1;AF=0.5;AN=2;AT=>31>33>34,>31>32>34;NS=1;PA=0;PL=5;PR=5;RC=x;RD=1;RL=8;RS=1;LV=2;PS=>2>5' +# expected: 'INFO tags correct for level-2 site of double-nested SNP' +0a1,2 +> A#1#y0 3 >2>5 A T AC=2;AF=0.5;AN=4;AT=>2>4>5,>2>3>5;NS=2;PA=1;PL=7;PR=1;RC=x;RD=1;RL=7;RS=1;LV=1;PS=>1>6 0|1 0|1 +> x 1 >1>6 C CAAGAAG,CATG,CAAG AC=1,2,1;AF=0.25,0.5,0.25;AN=4;AT=>1>6,>1>2>4>5>2>4>5>6,>1>2>3>5>6,>1>2>4>5>6;NS=2;PA=0;PL=1;PR=1;RC=x;RD=1;RL=1;RS=1;LV=0 1|2 3|2 +not ok 37 - nested deconstruction handles cycle +# got: '1' +# expected: '0' +Failed 30/37 subtests +t/27_vg_genotype.t: line 11: 3286937 Illegal instruction vg construct -v tiny/tiny.vcf.gz -r tiny/tiny.fa > tiny.vg +t/27_vg_genotype.t: line 12: 3286938 Illegal instruction vg index -x tiny.vg.xg -g tiny.vg.gcsa -k 16 tiny.vg +t/27_vg_genotype.t: line 13: 3286939 Illegal instruction vg sim -n 100 -x tiny.vg.xg -l 30 > reads.txt +t/27_vg_genotype.t: line 14: 3286940 Illegal instruction vg map -T reads.txt -g tiny.vg.gcsa -x tiny.vg.xg > tiny.gam +t/27_vg_genotype.t: line 16: 3286941 Illegal instruction vg genotype tiny.vg tiny.gam > /dev/null +t/27_vg_genotype.t: line 19: 3286942 Illegal instruction vg genotype tiny.vg tiny.gam -v > /dev/null +t/27_vg_genotype.t: line 24: 3286944 Illegal instruction vg construct -r tiny/tiny.fa > flat.vg +t/27_vg_genotype.t: line 25: 3286945 Illegal instruction vg index -x flat.xg -g flat.gcsa -k 8 flat.vg +t/27_vg_genotype.t: line 28: 3286948 Illegal instruction vg construct -r flat1.fa > flat1.vg +t/27_vg_genotype.t: line 29: 3286949 Illegal instruction vg index -x flat1.xg flat1.vg +t/27_vg_genotype.t: line 33: 3286953 Illegal instruction vg construct -r flat2.fa > flat2.vg +t/27_vg_genotype.t: line 34: 3286954 Illegal instruction vg index -x flat2.xg flat2.vg +t/27_vg_genotype.t: line 36: 3286957 Illegal instruction vg map -x flat.xg -g flat.gcsa -G <(cat flat1.sim flat2.sim) > flat.gam +t/27_vg_genotype.t: line 37: 3286958 Illegal instruction vg genotype flat.vg flat.gam -t 1 > flat.loci +t/27_vg_genotype.t: line 39: 3286960 Illegal instruction vg msga -f flats.fa -b x + 3286961 | vg paths -d -v - + 3286962 | vg mod -n - + 3286963 | vg mod -c - > flat_msga.vg +t/27_vg_genotype.t: line 40: 3286964 Illegal instruction vg augment flat.vg -L flat.loci + 3286965 | vg paths -d -v - + 3286966 | vg mod -n - + 3286967 | vg mod -c - > flat_mod.vg +t/27_vg_genotype.t: line 46: 3286982 Illegal instruction vg view -q flat.loci + 3286983 | vg view -qJz - + 3286984 | vg view -q - > /dev/null +t/27_vg_genotype.t: line 51: 3286986 Illegal instruction vg construct -v call/bigins.vcf.gz -r tiny/tiny.fa > bigins.vg +t/27_vg_genotype.t: line 52: 3286987 Illegal instruction vg index -x bigins.vg.xg -g bigins.vg.gcsa -k 16 bigins.vg +t/27_vg_genotype.t: line 54: 3286989 Illegal instruction vg map -T reads.txt -g bigins.vg.gcsa -x bigins.vg.xg > bigins.gam +t/27_vg_genotype.t .... +1..5 +not ok 1 - vg genotype runs successfully +# got: '132' +# expected: '0' +not ok 2 - vg genotype runs successfully when emitting vcf +# got: '132' +# expected: '0' +ok 3 - called genotypes are correct in a small simulated example +not ok 4 - genotype format can be converted to and from JSON +# got: '132' +# expected: '0' +not ok 5 - genotype finds big insert +# got: '0' +# expected: '1' +Failed 4/5 subtests +t/28_translate.t: line 10: 3286996 Illegal instruction vg construct -m 1000 -v tiny/tiny.vcf.gz -r tiny/tiny.fa > tiny.vg +t/28_translate.t: line 11: 3286997 Illegal instruction vg index -x tiny.xg -g tiny.gcsa -k 16 tiny.vg +t/28_translate.t: line 12: 3286998 Illegal instruction vg sim -n 5 -e 0.01 -i 0.005 -x tiny.xg -l 30 -a -s 1 + 3286999 | vg view -a - + 3287000 Done | sort + 3287001 | vg view -JGa - > tiny.sim +t/28_translate.t: line 13: 3287002 Illegal instruction vg map -G tiny.sim -x tiny.xg -g tiny.gcsa -t 1 > tiny.gam +t/28_translate.t: line 14: 3287003 Illegal instruction vg augment -Z tiny.trans -i tiny.vg tiny.gam > tiny.mod.vg +t/28_translate.t: line 15: 3287004 Illegal instruction vg paths -v tiny.mod.vg -X + 3287005 | vg view -a - + 3287006 Exit 1 | grep -v x + 3287007 Done | sort + 3287008 | vg view -JGa - > tiny.paths.gam +t/28_translate.t: line 16: 3287009 Illegal instruction vg translate -a tiny.paths.gam tiny.trans + 3287010 | vg view -a - + 3287011 Done | sort + 3287012 | vg view -JGa - > tiny.paths.trans.gam +t/28_translate.t: line 17: 3287013 Illegal instruction vg augment -Z tiny.trans.1 -i tiny.vg tiny.paths.trans.gam > tiny.mod.vg.1 +t/28_translate.t: line 23: 3287033 Illegal instruction vg construct -m 1000 -r tiny/tiny.fa > flat.vg +t/28_translate.t: line 24: 3287034 Illegal instruction vg index -x flat.xg -g flat.gcsa -k 8 flat.vg +t/28_translate.t: line 25: 3287035 Illegal instruction vg map -x flat.xg -g flat.gcsa -G tiny/flat-s69-n1-l50-e0.05.gam > flat.gam +t/28_translate.t: line 26: 3287036 Illegal instruction vg augment -i -Z flat1.trans flat.vg flat.gam > flat1.vg +t/28_translate.t: line 27: 3287037 Illegal instruction vg index -x flat1.xg -g flat1.gcsa -k 8 flat1.vg +t/28_translate.t: line 28: 3287038 Illegal instruction vg map -x flat1.xg -g flat1.gcsa -G tiny/flat1-s77-n1-l50-e0.05.gam > flat1.gam +t/28_translate.t: line 29: 3287039 Illegal instruction vg augment -i -Z flat2.trans flat1.vg flat1.gam > flat2.vg +t/28_translate.t: line 30: 3287040 Illegal instruction vg translate -o flat2.trans flat1.trans > flatover.trans +t/28_translate.t: line 31: 3287041 Illegal instruction vg paths -v flat2.vg -X + 3287042 | vg view -a - + 3287043 Exit 1 | grep -v x + 3287044 | vg view -JGa - > flat2.paths.gam +t/28_translate.t: line 32: 3287045 Illegal instruction vg translate -a flat2.paths.gam flatover.trans > flatback.gam +t/28_translate.t: line 33: 3287046 Illegal instruction vg augment -i flat.vg flatback.gam > flat2back.vg +t/28_translate.t ...... +1..2 +ok 1 - alignments used to modify a graph may be projected back to the original graph and used to regenerate the same graph +not ok 2 - translation overlay works and produces a sane result +# got: 'd41d8cd98f00b204e9800998ecf8427e' +# expected: '3ce4390abe667b24eb5148e216a2f5ec' +Failed 1/2 subtests +t/30_vg_chunk.t: line 11: 3287056 Illegal instruction vg construct -m 1000 -r small/x.fa -v small/x.vcf.gz -a > x.vg +t/30_vg_chunk.t: line 12: 3287057 Illegal instruction vg index -x x.xg x.vg +t/30_vg_chunk.t: line 13: 3287058 Illegal instruction vg gbwt -x x.vg -v small/x.vcf.gz -o x.haps.gbwt +t/30_vg_chunk.t: line 14: 3287059 Illegal instruction vg gbwt -x x.vg -E -o x.paths.gbwt +t/30_vg_chunk.t: line 15: 3287060 Illegal instruction vg gbwt -m x.haps.gbwt x.paths.gbwt -o x.gbwt +t/30_vg_chunk.t: line 16: 3287061 Illegal instruction vg gbwt -x x.vg x.gbwt --gbz-format -g x.gbz +t/30_vg_chunk.t: line 18: 3287062 Illegal instruction vg view -a small/x-l100-n1000-s10-e0.01-i0.01.gam > x.gam.json +t/30_vg_chunk.t: line 29: 3287089 Illegal instruction vg snarls x.xg > x.snarls +t/30_vg_chunk.t: line 38: 3287110 Illegal instruction vg chunk -x x.xg -p x -s 233 -o 50 -b _chunk_test -c 0 -t 2 +t/30_vg_chunk.t: line 39: 3287111 Illegal instruction vg chunk -x x.xg -p x -s 233 -o 50 -b _chunk_test -c 0 -t 1 +ls: cannot access '_chunk_test*.vg': No such file or directory +t/30_vg_chunk.t: line 44: 3287116 Illegal instruction vg gamsort small/x-l100-n1000-s10-e0.01-i0.01.gam -i x.sorted.gam.gai > x.sorted.gam +t/30_vg_chunk.t: line 46: 3287117 Illegal instruction vg chunk -x x.xg -a x.sorted.gam -g -b _chunk_test -e _chunk_test_bed.bed -E _chunk_test_out.bed -c 0 +ls: cannot access '_chunk_test*.vg': No such file or directory +ls: cannot access '_chunk_test*.gam': No such file or directory +grep: _chunk_test_out.bed: No such file or directory +t/30_vg_chunk.t: line 55: 3287139 Illegal instruction vg chunk -a small/x-l100-n1000-s10-e0.01-i0.01.gam -m 100 -b _chunk_test +ls: cannot access '_chunk_test*.gam': No such file or directory +t/30_vg_chunk.t: line 83: 3287202 Illegal instruction vg construct -m 1000 -r small/x.fa -v small/x.vcf.gz > x.vg +t/30_vg_chunk.t: line 85: 3287204 Illegal instruction vg chunk -x x.xg -n 5 -b x.chunk/ -O vg +cat: 'x.chunk/*vg': No such file or directory +t/30_vg_chunk.t: line 94: 3287221 Illegal instruction vg construct -r small/xy.fa -v small/xy.vcf.gz > xy.vg +t/30_vg_chunk.t: line 95: 3287222 Illegal instruction vg construct -r small/xy.fa -v small/xy.vcf.gz -R x > x.vg +t/30_vg_chunk.t: line 96: 3287223 Illegal instruction vg construct -r small/xy.fa -v small/xy.vcf.gz -R y > y.vg +t/30_vg_chunk.t: line 97: 3287224 Illegal instruction vg ids -j x.vg y.vg +t/30_vg_chunk.t: line 98: 3287225 Illegal instruction vg sim -x x.vg -n 50 -a > x.gam +t/30_vg_chunk.t: line 99: 3287226 Illegal instruction vg sim -x y.vg -n 100 -a > y.gam +t/30_vg_chunk.t: line 102: 3287228 Illegal instruction vg chunk -x xy.vg -M -b path_chunk -O hg -a xy.gam -g +t/30_vg_chunk.t: line 111: 3287261 Illegal instruction vg chunk -x xy.vg -C -p x -b path_chunk_ind -O hg -a xy.gam -g > /dev/null +t/30_vg_chunk.t: line 112: 3287262 Illegal instruction vg chunk -x xy.vg -C -p y -b path_chunk_ind -O hg -a xy.gam -g > /dev/null +t/30_vg_chunk.t: line 115: 3287275 Illegal instruction vg paths -v x.vg -E > x_paths.txt +t/30_vg_chunk.t: line 116: 3287276 Illegal instruction vg paths -v path_chunk_x.vg -E > pc_x_paths.txt +t/30_vg_chunk.t: line 119: 3287278 Illegal instruction vg chunk -x xy.vg -C -b components_chunk +t/30_vg_chunk.t ....... +1..32 +not ok 1 - unnamed test +# got: '210' +# expected: 'vg chunk with no options preserves nodes' +not ok 2 - unnamed test +# got: '291' +# expected: 'vg chunk with no options preserves edges' +not ok 3 - chunk has path going through node 9 +# got: '0' +# expected: '1' +not ok 4 - chunk can be found from GBZ +# got: '0' +# expected: '1' +not ok 5 - unnamed test +# got: '6789' +# expected: 'snarl chunk works on simple example' +not ok 6 - chunk has path going through node 9 +# got: '0' +# expected: '1' +not ok 7 - -s produces correct number of chunks +# got: '0' +# expected: '6' +not ok 8 - gam chunker produces correct number of graphs +# got: '0' +# expected: '2' +not ok 9 - gam chunker produces correct number of gams +# got: '0' +# expected: '2' +not ok 10 - gam chunker produces bed with correct number of chunks +# got: '0' +# expected: '2' +ok 11 - gam chunker emits each matching read at most once +not ok 12 - chunk contains the expected number of alignments +# got: '0' +# expected: '225' +not ok 13 - simple gam chunker produces correct number of gams +# got: '0' +# expected: '10' +not ok 14 - simple chunk contains the expected number of alignments +# got: '0' +# expected: '100' +not ok 15 - id chunker produces correct chunk size +# got: '0' +# expected: '3' +not ok 16 - id chunker produces correct single chunk +# got: '0' +# expected: '1' +not ok 17 - id chunker traces correct chunk size without haplotypes +# got: '0' +# expected: '5' +not ok 18 - id chunker traces correct chunk size +# got: '0' +# expected: '5' +ok 19 - chunker extracts no threads from an empty gPBWT +not ok 20 - chunker extracts 2 local threads from a gBWT with 2 locally distinct threads in it +# got: '0' +# expected: '2' +not ok 21 - chunker can extract a partial haplotype from a GBWT +# got: '' +# expected: '3' +not ok 22 - chunker can extract a partial haplotype from a GBZ +# got: '' +# expected: '3' +ok 23 - chunker doesn't see haplotypes in the GBZ if asked not to +ok 24 - trace consistent on path coordinates +ok 25 - n-chunking works and chunks over the full graph +ok 26 - path-based components finds subgraphs +ok 27 - x gam chunk has correct number of reads +ok 28 - y gam chunk has correct number of reads +ok 29 - x gam chunk has correct number of reads with -p path +ok 30 - y gam chunk has correct number of reads with -p path +ok 31 - path-based component contains correct path length +ok 32 - components finds subgraphs +Failed 20/32 subtests +t/31_vg_add.t: line 10: 3287292 Illegal instruction vg construct -r add/ref.fa > ref.vg +t/31_vg_add.t: line 11: 3287293 Illegal instruction vg add -v add/benedict.vcf ref.vg > benedict.vg +t/31_vg_add.t: line 14: 3287294 Illegal instruction vg add -v add/rename.vcf -n chrR=ref ref.vg > benedict2.vg +t/31_vg_add.t: line 20: 3287296 Illegal instruction vg convert -p ref.vg > ref.pg +t/31_vg_add.t: line 21: 3287297 Illegal instruction vg add -v add/benedict.vcf ref.pg > benedict3.vg +t/31_vg_add.t: line 27: 3287299 Illegal instruction vg add -v add/separated.vcf ref.vg > no-n.vg +t/31_vg_add.t: line 28: 3287300 Illegal instruction vg construct -r add/refN.fa > refN.vg +t/31_vg_add.t: line 29: 3287301 Illegal instruction vg add -v add/separated.vcf refN.vg > with-n.vg +t/31_vg_add.t: line 33: 3287310 Illegal instruction vg construct -r add/ngap.fa > ngap.vg +t/31_vg_add.t: line 34: 3287311 Illegal instruction vg add -v add/ngap-offset.vcf ngap.vg > ngap-add.vg +t/31_vg_add.t: line 39: 3287324 Illegal instruction vg construct -r small/x.fa > x-ref.vg +t/31_vg_add.t: line 40: 3287325 Illegal instruction vg add -v small/x.vcf.gz x-ref.vg > x.vg +t/31_vg_add.t ......... +1..12 +not ok 1 - vg add can create a graph +# got: '132' +# expected: '0' +not ok 2 - vg add can create a graph with contig renames +# got: '132' +# expected: '0' +ok 3 - vg add produces the same graph from VCFs with different contig names +not ok 4 - vg add can create a graph from a PackedGraph +# got: '132' +# expected: '0' +ok 5 - vg add produces the same graph from the same input in different formats +ok 6 - having reference Ns does not affect the graph topology +not ok 7 - adding variants adds only the alt bases near large N gaps +# got: '' +# expected: '73315' +not ok 8 - vg add can create a slightly larger graph +# got: '132' +# expected: '0' +ok 9 - ranks are calculated for emitted paths +not ok 10 - graphs with backward nodes can be added to +# got: '' +# expected: '5' +not ok 11 - graphs with multiple overlapping paths nodes can be added to +# got: '' +# expected: '5' +not ok 12 - graphs with backward and forward nodes can be added to +# got: '' +# expected: '5' +Failed 8/12 subtests +t/32_vg_snarls.t: line 10: 3287347 Illegal instruction vg view -J -v snarls/snarls.json > snarls.vg +t/32_vg_snarls.t: line 11: 3287348 Illegal instruction vg snarls -t 1 snarls.vg -r st.pb > snarls.pb +t/32_vg_snarls.t: line 18: 3287360 Illegal instruction vg index snarls.vg -x snarls.xg +t/32_vg_snarls.t: line 25: 3287369 Illegal instruction vg construct -Saf -v tiny/tiny.vcf.gz -r tiny/tiny.fa > tiny.vg +t/32_vg_snarls.t: line 26: 3287370 Illegal instruction vg snarls tiny.vg -r tiny.exhaustive.trav > /dev/null +t/32_vg_snarls.t: line 27: 3287371 Illegal instruction vg snarls tiny.vg -r tiny.vcf.trav -v tiny/tiny.vcf.gz > /dev/null +t/32_vg_snarls.t: line 36: 3287378 Illegal instruction vg construct -Saf -v sv/x.inv.vcf -r sv/x.fa > x.inv.vg +t/32_vg_snarls.t: line 37: 3287379 Illegal instruction vg snarls x.inv.vg -a -r x.inv.exhaustive.trav > /dev/null +t/32_vg_snarls.t: line 38: 3287380 Illegal instruction vg snarls x.inv.vg -a -r x.inv.vcf.trav -v sv/x.inv.vcf -f sv/x.fa > /dev/null +t/32_vg_snarls.t: line 47: 3287387 Illegal instruction vg construct -Saf -v ins_and_del/ins_and_del.vcf.gz -r ins_and_del/ins_and_del.fa > ins_and_del.vg +t/32_vg_snarls.t: line 48: 3287388 Illegal instruction vg snarls ins_and_del.vg -r ins_and_del.exhaustive.trav > /dev/null +t/32_vg_snarls.t: line 49: 3287389 Illegal instruction vg snarls ins_and_del.vg -r ins_and_del.vcf.trav -v ins_and_del/ins_and_del.vcf.gz > /dev/null +t/32_vg_snarls.t: line 58: 3287396 Illegal instruction vg construct -r small/xy.fa -v small/xy.vcf.gz > xy.vg +t/32_vg_snarls.t: line 59: 3287397 Illegal instruction vg construct -r small/xy.fa -v small/xy.vcf.gz -R x > x.vg +t/32_vg_snarls.t: line 60: 3287398 Illegal instruction vg construct -r small/xy.fa -v small/xy.vcf.gz -R y > y.vg +t/32_vg_snarls.t: line 61: 3287399 Illegal instruction vg snarls x.vg > xy.snarls +t/32_vg_snarls.t: line 62: 3287400 Illegal instruction vg snarls y.vg >> xy.snarls +t/32_vg_snarls.t: line 68: 3287413 Illegal instruction vg gbwt -g graph.gbz --gbz-format -G graphs/components_walks.gfa +t/32_vg_snarls.t: line 69: 3287414 Illegal instruction vg snarls -T graph.gbz > graph.snarls +t/32_vg_snarls.t: line 76: 3287419 Illegal instruction vg view -J -v snarls/nested.json > nested.vg +t/32_vg_snarls.t: line 77: 3287420 Illegal instruction vg snarls -t 1 -T nested.vg > nested.snarls +t/32_vg_snarls.t: line 93: 3287436 Illegal instruction vg autoindex -p index -g graphs/big_snarl_named.gfa -w giraffe +t/32_vg_snarls.t: line 94: 3287437 Illegal instruction vg snarls index.giraffe.gbz --traversals traversals.dat > /dev/null +t/32_vg_snarls.t: line 99: 3287446 Illegal instruction vg snarls index.giraffe.gbz --traversals traversals.dat --named-coordinates > /dev/null +t/32_vg_snarls.t ...... +1..19 +not ok 1 - vg snarls made right number of protobuf Snarls +# got: '0' +# expected: '3' +not ok 2 - vg snarls made right number of protobuf SnarlTraversals +# got: '0' +# expected: '6' +not ok 3 - unnamed test +# got: '1,3,7,' +# expected: 'vg snarls made snarls in the right order' +not ok 4 - vg snarls on xg made right number of protobuf Snarls +# got: '0' +# expected: '3' +not ok 5 - vg snarls on xg made right number of protobuf SnarlTraversals +# got: '0' +# expected: '6' +ok 6 - vcf traversals are the same as exhaustive traversals for tiny graph +ok 7 - vcf traversals are the same as exhaustive traversals for inversion +ok 8 - vcf traversals are the same as exhaustive traversals for ins_and_del graph +not ok 9 - correct number of snarls when parallelizing on compoents +# got: '0' +# expected: '35' +ok 10 - same number of snarls when parallelizing on components +not ok 11 - GBZ graphs can be used for finding snarls +# got: '132' +# expected: '0' +not ok 12 - correct number of snarls in the GFA W-line example +# got: '0' +# expected: '5' +not ok 13 - vg snarls made the right snarls when dealing with nested chains +# got: '1' +# expected: '15' +not ok 14 - vg snarls made snarls in the right order when dealing with nested chains +# got: '1' +# expected: '0' +not ok 15 - Correct snarls are found in GFA space +# got: '' +# expected: '["cats",null,"goldfish",null] +# ["goldfish",null,"sparrows",null] +# ["pigs",true,"squirrels",null] +# ["squirrels",null,"rabbits",true]' +not ok 16 - In node ID space traversal visits 7 nodes +# got: '0' +# expected: '7' +not ok 17 - In node ID space traversal visits 4 trivial snarls +# got: '0' +# expected: '4' +not ok 18 - In segment name space traversal visits 3 segments +# got: '0' +# expected: '3' +ok 19 - In segment name space traversal visits 0 trivial snarls +Failed 14/19 subtests +t/33_vg_mpmap.t: line 13: 3287457 Illegal instruction vg construct -m 1000 -a -r small/xy.fa -v small/xy2.vcf.gz > xy2.vg +t/33_vg_mpmap.t: line 14: 3287458 Illegal instruction vg index -x xy2.xg -g xy2.gcsa -v small/xy2.vcf.gz --gbwt-name xy2.gbwt -k 16 xy2.vg +t/33_vg_mpmap.t: line 25: 3287479 Illegal instruction vg mpmap -B -P 1 -n dna -I 200 -D 200 -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -f reads/xy2.matchpaired.fq -i -F GAM -t 1 > gbwt.gam +t/33_vg_mpmap.t: line 36: 3287489 Illegal instruction vg snarls xy2.vg > xy2.snarls +t/33_vg_mpmap.t: line 47: 3287507 Illegal instruction vg index -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -k 16 graphs/refonly-lrc_kir.vg +t/33_vg_mpmap.t: line 49: 3287508 Illegal instruction vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -I 10 -D 50 -F GAM -t 1 + 3287509 | vg view -aj - > temp_paired_alignment.json +t/33_vg_mpmap.t: line 50: 3287510 Illegal instruction vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -I 100000 -D 5 -F GAM -t 1 + 3287511 | vg view -aj - > temp_distant_alignment.json +t/33_vg_mpmap.t: line 51: 3287512 Illegal instruction vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -F GAM -t 1 + 3287513 | vg view -aj - > temp_independent_alignment.json +t/33_vg_mpmap.t: line 64: 3287545 Illegal instruction vg sim -x graphs/refonly-lrc_kir.vg.xg -n 1000 -p 500 -l 100 -a > input.gam +t/33_vg_mpmap.t: line 66: 3287546 Illegal instruction 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 > output.gam +t/33_vg_mpmap.t: line 73: 3287552 Illegal instruction vg construct -m 1000 -r tiny/tiny.fa -v tiny/tiny.vcf.gz > t.vg +t/33_vg_mpmap.t: line 74: 3287553 Illegal instruction vg index -x t.xg -g t.gcsa -k 16 t.vg +rm: cannot remove 't.xg': No such file or directory +rm: cannot remove 't.gcsa': No such file or directory +rm: cannot remove 't.gcsa.lcp': No such file or directory +t/33_vg_mpmap.t: line 95: 3287559 Illegal instruction vg construct -m 32 -r small/x.fa -v small/x.vcf.gz > s.vg +t/33_vg_mpmap.t: line 96: 3287560 Illegal instruction vg snarls -T s.vg > s.snarls +t/33_vg_mpmap.t: line 97: 3287561 Illegal instruction vg index s.vg -x s.xg -g s.gcsa +t/33_vg_mpmap.t: line 98: 3287562 Illegal instruction vg index s.vg -j s.dist +rm: cannot remove 's.xg': No such file or directory +rm: cannot remove 's.gcsa': No such file or directory +rm: cannot remove 's.gcsa.lcp': No such file or directory +rm: cannot remove 's.dist': No such file or directory +t/33_vg_mpmap.t: line 135: 3287583 Illegal instruction vg construct -r small/x.fa > x.vg +t/33_vg_mpmap.t: line 136: 3287584 Illegal instruction vg sim -a -p 200 -v 10 -l 50 -n 1000 -s 12345 -x x.vg > x.gam +t/33_vg_mpmap.t: line 138: 3287585 Illegal instruction vg construct -r small/xy.fa > xy.vg +t/33_vg_mpmap.t: line 139: 3287586 Illegal instruction vg snarls -T xy.vg > xy.snarls +t/33_vg_mpmap.t: line 140: 3287587 Illegal instruction vg index xy.vg -x xy.xg -g xy.gcsa +t/33_vg_mpmap.t: line 141: 3287588 Illegal instruction vg index xy.vg -j xy.dist +t/33_vg_mpmap.t: line 143: 3287589 Illegal instruction vg mpmap -x xy.xg -d xy.dist -g xy.gcsa -G x.gam -F SAM -i --frag-mean 50 --frag-stddev 10 -M 1 > xy.sam +t/33_vg_mpmap.t: line 152: 3287596 Illegal instruction vg mpmap -x xy.xg -d xy.dist -g xy.gcsa -G x.gam -F SAM -M 1 > xy.sam +rm: cannot remove 'xy.xg': No such file or directory +rm: cannot remove 'xy.gcsa': No such file or directory +rm: cannot remove 'xy.dist': No such file or directory +t/33_vg_mpmap.t ....... +1..21 +not ok 1 - MAPQ is 50% without haplotype info +# got: '' +# expected: '3' +not ok 2 - haplotype match can disambiguate +# got: '' +# expected: '4' +not ok 3 - MAPQs are computed for all multimappings +# got: '' +# expected: '2' +not ok 4 - MAPQ is 50% when paired without haplotype info +# got: '' +# expected: '3' +not ok 5 - haplotype match can disambiguate paired +# got: '' +# expected: '4' +not ok 6 - use of haplotype-aware mapping is recorded +# got: '' +# expected: 'true' +not ok 7 - Haplotype-oblivious mapping places read on the wrong contig +# got: '' +# expected: '50' +not ok 8 - Haplotype-oblivious mapping places read with MAPQ of 50% +# got: '' +# expected: '3' +not ok 9 - Haplotype-aware mapping places read on the right contig +# got: '' +# expected: '1' +not ok 10 - Haplotype-aware mapping places read with MAPQ > 50% +# got: '' +# expected: '6' +not ok 11 - paired read alignments forced to be consistent have lower score than unrestricted alignments +# got: '0' +# expected: '1' +not ok 12 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments +# got: '0' +# expected: '1' +not ok 13 - paired read alignments forced to be near each other are closer together in node id space than those forced to be far apart +# got: '0' +# expected: '1' +ok 14 - small batches are still all paired in the output +not ok 15 - multipath mapping works in scenarios that trigger branch point trimming +# got: '0' +# expected: '3' +not ok 16 - spliced alignments can be found when aligning RNA +# got: '' +# expected: '105' +not ok 17 - paired mapping can identify a splice junction on read 1 +# got: '0' +# expected: '1' +not ok 18 - paired mapping can identify a splice junction on read 2 +# got: '0' +# expected: '1' +not ok 19 - HTS output contains group mapq annotation +# got: '0' +# expected: '2' +not ok 20 - paired reads are evenly split between equivalent mappings +# got: '0' +# expected: '1' +not ok 21 - unpaired reads are evenly split between equivalent mappings +# got: '0' +# expected: '1' +Dubious, test returned 1 (wstat 256, 0x100) +Failed 20/21 subtests +t/34_vg_pack.t: line 10: 3287605 Illegal instruction vg construct -m 1000 -r tiny/tiny.fa > flat.vg +t/34_vg_pack.t: line 11: 3287606 Illegal instruction vg view flat.vg + 3287607 Done | sed 's/CAAATAAGGCTTGGAAATTTTCTGGAGTTCTATTATATTCCAACTCTCTG/CAAATAAGGCTTGGAAATTTTCTGGAGATCTATTATACTCCAACTCTCTG/' + 3287608 | vg view -Fv - > 2snp.vg +t/34_vg_pack.t: line 12: 3287609 Illegal instruction vg index -x 2snp.xg 2snp.vg +t/34_vg_pack.t: line 13: 3287610 Illegal instruction vg sim -l 30 -x 2snp.xg -n 30 -a > 2snp.sim +t/34_vg_pack.t: line 14: 3287611 Illegal instruction vg index -x flat.xg -g flat.gcsa -k 16 flat.vg +t/34_vg_pack.t: line 15: 3287612 Illegal instruction vg map -g flat.gcsa -x flat.xg -G 2snp.sim -k 8 > 2snp.gam +t/34_vg_pack.t: line 16: 3287613 Illegal instruction vg pack -x flat.xg -o 2snp.gam.cx -g 2snp.gam -e +t/34_vg_pack.t: line 20: 3287620 Illegal instruction vg pack -x flat.xg -o 2snp.gam.snapshot.cx -g pileup/2snp.gam -e +t/34_vg_pack.t: line 25: 3287636 Illegal instruction vg pack -x flat.xg -i 2snp.gam.cx -i 2snp.gam.cx -i 2snp.gam.cx -o 2snp.gam.cx.3x +(standard_in) 1: syntax error +(standard_in) 1: syntax error +(standard_in) 1: syntax error +(standard_in) 1: syntax error +t/34_vg_pack.t: line 32: 3287672 Illegal instruction vg pack -x flat.xg -o 2snp.gam.cx -b 10 -g 2snp.gam +t/34_vg_pack.t: line 44: 3287692 Illegal instruction vg pack -x flat.xg -o 2snp.gam.cx -g 2snp.gam +t/34_vg_pack.t: line 45: 3287693 Illegal instruction vg pack -x flat.xg -o 2snp.gam.cx.3x -i 2snp.gam.cx -i 2snp.gam.cx -i 2snp.gam.cx +t/34_vg_pack.t: line 47: 3287697 Done cat 2snp.gam 2snp.gam 2snp.gam + 3287698 Illegal instruction | vg pack -x flat.xg -o 2snp.gam.cx -g - +t/34_vg_pack.t: line 52: 3287702 Illegal instruction vg pack -x flat.xg -o 2snp.gam.cx -g 2snp.gam +t/34_vg_pack.t: line 53: 3287703 Illegal instruction vg pack -x flat.xg -o 2snp.gam.cx.3x -i 2snp.gam.cx -i 2snp.gam.cx -i 2snp.gam.cx +t/34_vg_pack.t: line 55: 3287707 Done cat 2snp.gam 2snp.gam 2snp.gam + 3287708 Illegal instruction | vg pack -x flat.xg -o 2snp.gam.cx -g - +t/34_vg_pack.t: line 62: 3287713 Illegal instruction vg construct -r tiny/tiny.fa -v tiny/tiny.vcf.gz > tiny.vg +t/34_vg_pack.t: line 63: 3287714 Illegal instruction vg index tiny.vg -x tiny.xg +t/34_vg_pack.t: line 73: 3287731 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > x.vg +t/34_vg_pack.t: line 74: 3287732 Illegal instruction vg index -x x.xg x.vg +t/34_vg_pack.t: line 75: 3287733 Illegal instruction vg sim -s 1 -n 1000 -l 150 -x x.xg -a > sim.gam +t/34_vg_pack.t: line 76: 3287734 Illegal instruction vg pack -x x.xg -g sim.gam -o x.xg.cx +t/34_vg_pack.t: line 77: 3287735 Illegal instruction vg pack -x x.vg -g sim.gam -o x.vg.cx -t 1 +t/34_vg_pack.t: line 96: 3287755 Illegal instruction vg convert x.vg -G sim.gam + 3287756 Broken pipe | bgzip + 3287757 | vg pack -x x.vg -a - -o x.vg.gaf.cx +t/34_vg_pack.t: line 107: 3287766 Illegal instruction vg construct -m 5 -r tiny/tiny.fa > flat.vg +t/34_vg_pack.t: line 108: 3287767 Illegal instruction vg index flat.vg -g flat.gcsa +t/34_vg_pack.t: line 110: 3287768 Illegal instruction vg map -x flat.vg -g flat.gcsa -s CAAATAAGG + 3287769 | vg view -a - + 3287770 Done | sed -e 's/60/20/g' + 3287771 | vg view -JaG - > flat.gam +t/34_vg_pack.t: line 112: 3287772 Illegal instruction vg map -x flat.vg -g flat.gcsa -s GGCTTGGAA + 3287773 | vg view -a - + 3287774 Done | sed -e 's/60/10/g' + 3287775 | vg view -JaG - >> flat.gam +t/34_vg_pack.t: line 114: 3287776 Illegal instruction vg map -x flat.vg -g flat.gcsa -s AACTCTCTG + 3287777 | vg view -a - + 3287778 | vg view -JaG - >> flat.gam +t/34_vg_pack.t: line 115: 3287779 Illegal instruction vg pack -x flat.vg -o flat.cx -g flat.gam +t/34_vg_pack.t: line 120: 3287787 Illegal instruction vg map -x flat.vg -g flat.gcsa -s CAAATAAGGCTTGGAAATTTTCTGGAGTTCTATTATATTCCAACTCTCTG > span2.gam +t/34_vg_pack.t: line 121: 3287788 Illegal instruction vg map -x flat.vg -g flat.gcsa -s CAGAGAGTTGGAATATAATAGAACTCCAGAAAATTTCCAAGCCTTATTTG >> span2.gam +t/34_vg_pack.t: line 122: 3287789 Illegal instruction vg pack -x flat.vg -g span2.gam -o span2.pack +t/34_vg_pack.t: line 123: 3287790 Illegal instruction vg pack -x flat.vg -g span2.gam -s 10 -o span2.s10.pack +t/34_vg_pack.t: line 133: 3287804 Illegal instruction vg pack -x flat.vg -g span2.gam -s 9 -o span2.s9.pack +t/34_vg_pack.t ........ +1..20 +not ok 1 - allele observation packing detects 2 SNPs +# got: '0' +# expected: '2' +not ok 2 - pileup packs agree with graph coverage +# got: 'f9108e41700ebf9a7be4b41322033704' +# expected: 'd41d8cd98f00b204e9800998ecf8427e' +not ok 3 - unnamed test +# got: 'graph coverages are merged from multiple .cx indexes' +# expected: '' +not ok 4 - unnamed test +# got: 'edit records are merged from multiple .cx indexes' +# expected: '' +ok 5 - binned edit accumulation does not affect the result +ok 6 - pack records are filtered by node id +ok 7 - pack records are filtered by node id +ok 8 - pack index merging produces the expected result +ok 9 - pack index merging produces the expected result for edges +not ok 10 - unnamed test +# got: '88' +# expected: 'pack computes the same total edge coverage as pileup' +not ok 11 - unnamed test +# got: 'pack stores the correct edge pileup to disk' +# expected: '' +ok 12 - node packs on vg same as xg +ok 13 - edge packs on vg same as xg +ok 14 - node packs same on vg when using 3 threads as when using 1 +ok 15 - edge packs same on vg when using 2 threads as when using 1 +ok 16 - node packs on gaf same as gam +ok 17 - edge packs on gaf same as gam +not ok 18 - unnamed test +# got: '20-15-10-10-0-0-0-0-60-60-' +# expected: 'average node qualities are correct' +1,20d0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +not ok 19 - pack -s 10 sets fist and last 10bp of coverage to 0 like expected +# got: '1' +# expected: '0' +1,18d0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +< 0 +not ok 20 - pack -s 9 sets fist and last 9bp of coverage to 0 like expected +# got: '1' +# expected: '0' +Failed 9/20 subtests +t/36_vg_annotate.t: line 10: 3287820 Illegal instruction vg construct -r tiny/tiny.fa -v tiny/tiny.vcf.gz > t.vg +t/36_vg_annotate.t: line 12: 3287821 Illegal instruction vg mod -N t.vg > t.ref.vg +t/36_vg_annotate.t: line 13: 3287822 Illegal instruction vg index -x t.xg t.vg +t/36_vg_annotate.t: line 14: 3287823 Illegal instruction vg index -x t.ref.xg t.ref.vg +t/36_vg_annotate.t: line 18: 3287828 Illegal instruction vg annotate -b tiny/tiny.bed -x t.ref.xg -a tiny/tiny-s543-n30-l10.gam > annotated.gam +t/36_vg_annotate.t: line 27: 3287861 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > x.vg +t/36_vg_annotate.t: line 28: 3287862 Illegal instruction vg index -x x.xg x.vg +t/36_vg_annotate.t: line 30: 3287863 Illegal instruction vg annotate -p -x x.xg -a small/x-s1337-n1.gam > annot.gam +t/36_vg_annotate.t: line 37: 3287875 Illegal instruction vg view -Jv cyclic/circular_path.json > circular_path.vg +t/36_vg_annotate.t: line 38: 3287876 Illegal instruction vg index -x circular_path.xg circular_path.vg +t/36_vg_annotate.t: line 39: 3287877 Illegal instruction vg annotate -p -x circular_path.xg -b cyclic/circular_path_origin.bed > circular_path_origin.gam +t/36_vg_annotate.t .... +1..9 +not ok 1 - we can detect when reads contain non-reference variation +# got: '0' +# expected: '10' +not ok 2 - vg annotate finds the right number of reads overlapping a feature +# got: '0' +# expected: '3' +ok 3 - all reads overlapping a feature fall on its node +ok 4 - vg annotate finds no reads touching both of two distant features +not ok 5 - vg annotate shows reads having to go through one feature to get to another at the end +# got: '0' +# expected: '2' +not ok 6 - vg annotate shows all reads overlapping a whole-reference-covering feature +# got: '0' +# expected: '30' +not ok 7 - annotating with earliest path position produces one position +# got: '0' +# expected: '1' +not ok 8 - annotating with multiple path positions produces multiple positions +# got: '0' +# expected: '13' +not ok 9 - annotations derived from BED can span the end/start joins of circular paths +# got: '' +# expected: '{"node_id":"1","offset":"5"} +# {"node_id":"1"}' +Failed 7/9 subtests +t/37_vg_gbwt.t: line 12: 3287884 Illegal instruction vg construct -r small/xy.fa -v small/xy2.vcf.gz -R x -C -a > x.vg 2> /dev/null +t/37_vg_gbwt.t: line 13: 3287885 Illegal instruction vg construct -r small/xy.fa -v small/xy2.vcf.gz -R y -C -a > y.vg 2> /dev/null +t/37_vg_gbwt.t: line 14: 3287886 Illegal instruction vg ids -j x.vg y.vg +t/37_vg_gbwt.t: line 16: 3287887 Illegal instruction vg index -x x.xg x.vg +t/37_vg_gbwt.t: line 17: 3287888 Illegal instruction vg index -x xy.xg x.vg y.vg +t/37_vg_gbwt.t: line 18: 3287889 Illegal instruction vg index -x xy-alt.xg -L x.vg y.vg +t/37_vg_gbwt.t: line 22: 3287890 Illegal instruction vg gbwt -x x.vg -o x.gbwt -v small/xy2.vcf.gz +t/37_vg_gbwt.t: line 24: 3287891 Illegal instruction vg index -G x2.gbwt -v small/xy2.vcf.gz x.vg +cmp: x.gbwt: No such file or directory +t/37_vg_gbwt.t: line 28: 3287893 Illegal instruction vg gbwt -x x.vg -o parse --parse-only -v small/xy2.vcf.gz +cmp: x.gbwt: No such file or directory +t/37_vg_gbwt.t: line 49: 3287911 Illegal instruction vg gbwt -E -o x.ref.gbwt -x x.vg +t/37_vg_gbwt.t: line 51: 3287912 Illegal instruction vg index -G x2.ref.gbwt -T x.vg +cmp: x.ref.gbwt: No such file or directory +t/37_vg_gbwt.t: line 61: 3287916 Illegal instruction vg paths -v x.vg -X -Q _alt > x.alts.gam +t/37_vg_gbwt.t: line 62: 3287917 Illegal instruction vg convert -G x.alts.gam x.vg > x.alts.gaf +t/37_vg_gbwt.t: line 63: 3287918 Illegal instruction vg gbwt -A -o x.alts.gaf.gbwt -x x.vg x.alts.gaf +t/37_vg_gbwt.t: line 65: 3287919 Illegal instruction vg index -F x.alts.gaf -G x2.alts.gaf.gbwt x.vg +cmp: x.alts.gaf.gbwt: No such file or directory +t/37_vg_gbwt.t: line 69: 3287921 Illegal instruction vg gbwt -A --gam-format -o x.alts.gam.gbwt -x x.vg x.alts.gam +cmp: x.alts.gaf.gbwt: No such file or directory +t/37_vg_gbwt.t: line 79: 3287925 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz -a --region x:100-200 > x.part.vg +t/37_vg_gbwt.t: line 80: 3287926 Illegal instruction vg gbwt -x x.part.vg -o x.part.gbwt --vcf-region x:100-200 -v small/x.vcf.gz 2> log.txt +t/37_vg_gbwt.t: line 83: 3287930 Illegal instruction vg index -G x2.part.gbwt --region x:100-200 -v small/x.vcf.gz x.part.vg 2> log.txt +cmp: x.part.gbwt: No such file or directory +t/37_vg_gbwt.t: line 92: 3287933 Illegal instruction vg gbwt -x x.vg -o x.gbwt -v small/xy2.vcf.gz +t/37_vg_gbwt.t: line 93: 3287934 Illegal instruction vg gbwt -x y.vg -o y.gbwt -v small/xy2.vcf.gz +t/37_vg_gbwt.t: line 94: 3287935 Illegal instruction vg gbwt -m -o xy.merge.gbwt x.gbwt y.gbwt +t/37_vg_gbwt.t: line 96: 3287936 Illegal instruction vg gbwt -f -o xy.fast.gbwt x.gbwt y.gbwt +cmp: xy.merge.gbwt: No such file or directory +t/37_vg_gbwt.t: line 100: 3287938 Illegal instruction vg gbwt -b --merge-jobs 1 -o xy.parallel.gbwt x.gbwt y.gbwt +cmp: xy.merge.gbwt: No such file or directory +t/37_vg_gbwt.t: line 104: 3287940 Illegal instruction vg gbwt -x xy-alt.xg -o xy.direct.gbwt -v small/xy2.vcf.gz +cmp: xy.direct.gbwt: No such file or directory +t/37_vg_gbwt.t: line 108: 3287942 Illegal instruction vg gbwt -x xy-alt.xg -o xy.multi.gbwt -v --inputs-as-jobs small/xy2_x.vcf.gz small/xy2_y.vcf.gz +cmp: xy.direct.gbwt: No such file or directory +t/37_vg_gbwt.t: line 114: 3287944 Illegal instruction vg gbwt -x xy-alt.xg -o xy.1000gp.gbwt --preset 1000gp -v small/xy2.vcf.gz +t/37_vg_gbwt.t: line 128: 3287951 Illegal instruction vg gbwt -E -o xy.contigs.gbwt -x xy.xg +t/37_vg_gbwt.t: line 130: 3287952 Illegal instruction vg index -G xy2.contigs.gbwt -T xy.xg +cmp: xy.contigs.gbwt: No such file or directory +t/37_vg_gbwt.t: line 144: 3287959 Illegal instruction vg gbwt -x xy-alt.xg -o xy.gbwt -r xy.ri --num-threads 1 -v small/xy2.vcf.gz +t/37_vg_gbwt.t: line 151: 3287961 Illegal instruction vg gbwt -x x.vg -o x.gbwt -v small/xy2.vcf.gz +t/37_vg_gbwt.t: line 155: 3287963 Illegal instruction vg gbwt -m -o x2.gbwt x.gbwt empty.gbwt +cmp: x.gbwt: No such file or directory +t/37_vg_gbwt.t: line 161: 3287965 Illegal instruction vg gbwt -m -o x2.gbwt empty.gbwt x.gbwt 2> /dev/null +cmp: x.gbwt: No such file or directory +t/37_vg_gbwt.t: line 167: 3287967 Illegal instruction vg gbwt -f -o x2.gbwt x.gbwt empty.gbwt +cmp: x.gbwt: No such file or directory +t/37_vg_gbwt.t: line 173: 3287969 Illegal instruction vg gbwt -f -o x2.gbwt empty.gbwt x.gbwt +cmp: x.gbwt: No such file or directory +t/37_vg_gbwt.t: line 179: 3287971 Illegal instruction vg gbwt -b --merge-jobs 1 -o x2.gbwt x.gbwt empty.gbwt +cmp: x.gbwt: No such file or directory +t/37_vg_gbwt.t: line 185: 3287973 Illegal instruction vg gbwt -b --merge-jobs 1 -o x2.gbwt empty.gbwt x.gbwt 2> /dev/null +cmp: x.gbwt: No such file or directory +t/37_vg_gbwt.t: line 194: 3287976 Illegal instruction vg gbwt -x xy-alt.xg -o xy.gbwt -v small/xy2.vcf.gz +t/37_vg_gbwt.t: line 195: 3287977 Illegal instruction vg gbwt -E -o xy.ref.gbwt -x xy.xg +t/37_vg_gbwt.t: line 196: 3287978 Illegal instruction vg gbwt -m -o xy.both.gbwt xy.gbwt xy.ref.gbwt +t/37_vg_gbwt.t: line 200: 3287980 Illegal instruction vg gbwt -R _gbwt_ref -o xy.removed.gbwt xy.both.gbwt +t/37_vg_gbwt.t: line 208: 3287985 Illegal instruction vg gbwt -o all.gbwt -G graphs/three_samples.gfa +t/37_vg_gbwt.t: line 213: 3287988 Illegal instruction vg gbwt -R sample1 -R sample3 -o removed.gbwt all.gbwt +t/37_vg_gbwt.t: line 222: 3287992 Illegal instruction vg gbwt -x x.vg -o x.gbwt -v small/xy2.vcf.gz +t/37_vg_gbwt.t: line 223: 3287993 Illegal instruction vg gbwt -e x.extract x.gbwt +cat: x.extract: No such file or directory +t/37_vg_gbwt.t: line 231: 3287998 Illegal instruction vg gbwt -x x.vg -g x.gg -o x.gbwt -v small/xy2.vcf.gz +md5sum: x.gg: No such file or directory +t/37_vg_gbwt.t: line 236: 3288002 Illegal instruction vg gbwt -x x.vg -g x.gbz --gbz-format x.gbwt +md5sum: x.gbz: No such file or directory +t/37_vg_gbwt.t: line 241: 3288006 Illegal instruction vg gbwt -x x.vg -g x2.gbz --gbz-format -v small/xy2.vcf.gz +cmp: x.gbz: No such file or directory +t/37_vg_gbwt.t: line 247: 3288008 Illegal instruction vg gbwt -I x.gg -g x3.gbz --gbz-format x.gbwt +cmp: x.gbz: No such file or directory +t/37_vg_gbwt.t: line 253: 3288010 Illegal instruction vg gbwt -o extracted.gbwt -Z x.gbz +cmp: x.gbwt: No such file or directory +t/37_vg_gbwt.t: line 259: 3288012 Illegal instruction vg gbwt -o extracted2.gbwt -g extracted2.gg -Z x.gbz +cmp: x.gbwt: No such file or directory +cmp: x.gg: No such file or directory +t/37_vg_gbwt.t: line 271: 3288017 Illegal instruction vg gbwt -P -n 16 -x xy.xg -g xy.cover.gg -o xy.cover.gbwt +md5sum: xy.cover.gg: No such file or directory +t/37_vg_gbwt.t: line 282: 3288026 Illegal instruction vg gbwt -P -n 16 -x xy.xg -g xy.cover.gg -o xy.cover.gbwt --pass-paths +md5sum: xy.cover.gg: No such file or directory +t/37_vg_gbwt.t: line 293: 3288035 Illegal instruction vg gbwt -x xy-alt.xg -g xy.local.gg -l -n 16 -o xy.local.gbwt -v small/xy2.vcf.gz +md5sum: xy.local.gg: No such file or directory +t/37_vg_gbwt.t: line 302: 3288043 Illegal instruction vg gbwt -x xy-alt.xg -g xy.local.gbz --gbz-format -l -n 16 --num-jobs 1 -v small/xy2.vcf.gz +md5sum: xy.local.gbz: No such file or directory +t/37_vg_gbwt.t: line 307: 3288047 Illegal instruction vg gbwt -x xy-alt.xg -g xy.local.gbz --gbz-format -l -n 16 --num-jobs 2 -v small/xy2.vcf.gz +md5sum: xy.local.gbz: No such file or directory +t/37_vg_gbwt.t: line 314: 3288052 Illegal instruction vg gbwt -x xy-alt.xg -g xy.local.gg -l -n 16 -o xy.local.gbwt -v small/xy2.vcf.gz --pass-paths +md5sum: xy.local.gg: No such file or directory +t/37_vg_gbwt.t: line 325: 3288061 Illegal instruction vg gbwt -G haplotype-sampling/micb-kir3dl1.gfa -g large.gbz --gbz-format +t/37_vg_gbwt.t: line 326: 3288062 Illegal instruction vg gbwt -Z large.gbz -l -n 16 --pass-paths -o large.local.gbwt +t/37_vg_gbwt.t: line 338: 3288071 Illegal instruction vg gbwt -x x.vg -o x.gbwt -v small/xy2.vcf.gz +t/37_vg_gbwt.t: line 339: 3288072 Illegal instruction vg gbwt -a -n 16 -x xy.xg -g augmented.gg -o augmented.gbwt x.gbwt +md5sum: augmented.gg: No such file or directory +t/37_vg_gbwt.t: line 355: 3288082 Illegal instruction vg gbwt -o gfa.gbwt -G graphs/components_walks.gfa +md5sum: gfa.gbwt: No such file or directory +t/37_vg_gbwt.t: line 364: 3288090 Illegal instruction vg gbwt -o gfa2.gbwt -g gfa2.gg --translation gfa2.trans -G graphs/components_walks.gfa +cmp: gfa.gbwt: No such file or directory +md5sum: gfa2.gg: No such file or directory +t/37_vg_gbwt.t: line 369: gfa2.trans: No such file or directory +t/37_vg_gbwt.t: line 372: 3288097 Illegal instruction vg gbwt -g gfa2.gbz --gbz-format -G graphs/components_walks.gfa +md5sum: gfa2.gbz: No such file or directory +t/37_vg_gbwt.t: line 377: 3288101 Illegal instruction vg gbwt -o chopping.gbwt -g chopping.gg --translation chopping.trans --max-node 2 -G graphs/chopping_walks.gfa +t/37_vg_gbwt.t: line 383: chopping.trans: No such file or directory +t/37_vg_gbwt.t: line 386: 3288108 Illegal instruction vg gbwt -g chopping.gbz --gbz-format --max-node 2 -G graphs/chopping_walks.gfa +t/37_vg_gbwt.t: line 387: 3288109 Illegal instruction vg gbwt -Z chopping.gbz -o /dev/null --translation from_gbz.trans +t/37_vg_gbwt.t: line 389: from_gbz.trans: No such file or directory +t/37_vg_gbwt.t: line 392: 3288112 Illegal instruction vg gbwt -o ref_paths.gbwt -g ref_paths.gg --translation ref_paths.trans -G graphs/components_paths_walks.gfa +t/37_vg_gbwt.t: line 398: ref_paths.trans: No such file or directory +t/37_vg_gbwt.t: line 406: 3288123 Illegal instruction vg gbwt -g gfa.gbz --gbz-format -G graphs/gfa_with_reference.gfa +t/37_vg_gbwt.t: line 408: 3288124 Illegal instruction vg gbwt -Z gfa.gbz --tags > tags.tsv +t/37_vg_gbwt.t: line 411: 3288131 Illegal instruction vg gbwt -g gfa2.gbz --gbz-format -Z gfa.gbz --set-tag "reference_samples=GRCh38 CHM13" +t/37_vg_gbwt.t: line 415: 3288144 Illegal instruction vg gbwt -g gfa2.gbz --gbz-format -Z gfa.gbz --set-tag "reference_samples=GRCh38#1 CHM13" 2> /dev/null +t/37_vg_gbwt.t: line 417: 3288145 Illegal instruction vg gbwt -g gfa3.gbz --gbz-format --set-reference GRCh37 --set-reference CHM13 -Z gfa2.gbz +t/37_vg_gbwt.t: line 424: 3288151 Illegal instruction vg gbwt -g gfa.gbz --gbz-format -G graphs/gfa_two_part_reference.gfa +t/37_vg_gbwt.t ........ +1..159 +not ok 1 - chromosome X GBWT with vg gbwt +# got: '132' +# expected: '0' +not ok 2 - chromosome X GBWT with vg index +# got: '132' +# expected: '0' +not ok 3 - identical construction results with vg gbwt and vg index +# got: '2' +# expected: '0' +not ok 4 - chromosome X VCF parse +# got: '132' +# expected: '0' +not ok 5 - chromosome X GBWT from VCF parse +# got: '1' +# expected: '0' +not ok 6 - identical construction results with vg gbwt and from VCF parse +# got: '2' +# expected: '0' +not ok 7 - unnamed test +# got: '2' +# expected: 'chromosome X: 2 threads' +not ok 8 - unnamed test +# got: '1' +# expected: 'chromosome X: 1 contig' +not ok 9 - unnamed test +# got: '2' +# expected: 'chromosome X: 2 haplotypes' +not ok 10 - unnamed test +# got: '1' +# expected: 'chromosome X: 1 sample' +not ok 11 - chromosome X: 2 thread names +# got: '0' +# expected: '2' +not ok 12 - chromosome X: 1 contig name +# got: '0' +# expected: '1' +not ok 13 - chromosome X: 1 sample name +# got: '0' +# expected: '1' +not ok 14 - chromosome X reference GBWT with vg gbwt +# got: '132' +# expected: '0' +not ok 15 - chromosome X reference GBWT with vg index +# got: '132' +# expected: '0' +not ok 16 - identical construction results with vg gbwt and vg index +# got: '2' +# expected: '0' +not ok 17 - unnamed test +# got: '1' +# expected: 'chromosome X reference: 1 thread' +not ok 18 - chromosome X GAF with vg gbwt +# got: '132' +# expected: '0' +not ok 19 - chromosome X GAF with vg index +# got: '132' +# expected: '0' +not ok 20 - identical construction results with vg gbwt and vg index +# got: '2' +# expected: '0' +not ok 21 - chromosome X GAM with vg gbwt +# got: '132' +# expected: '0' +not ok 22 - identical construction results from GAF and GAM +# got: '2' +# expected: '0' +not ok 23 - chromosome X subgraph GBWT with vg gbwt +# got: '132' +# expected: '0' +ok 24 - no warnings about missing variants +not ok 25 - chromosome X subgraph GBWT with vg index +# got: '132' +# expected: '0' +not ok 26 - identical construction results with vg gbwt and vg index +# got: '2' +# expected: '0' +not ok 27 - insertion merging with multiple chromosomes +# got: '132' +# expected: '0' +not ok 28 - fast merging with multiple chromosomes +# got: '132' +# expected: '0' +not ok 29 - identical merging results with the insertion and fast algorithms +# got: '2' +# expected: '0' +not ok 30 - parallel merging with multiple chromosomes +# got: '132' +# expected: '0' +not ok 31 - identical merging results with the insertion and parallel algorithms +# got: '2' +# expected: '0' +not ok 32 - direct construction with multiple chromosomes and a single VCF +# got: '132' +# expected: '0' +not ok 33 - identical results with direct construction and merging +# got: '2' +# expected: '0' +not ok 34 - direct construction with multiple chromosomes and multiple VCFs +# got: '132' +# expected: '0' +not ok 35 - identical construction results with a single VCF and multiple VCFs +# got: '2' +# expected: '0' +not ok 36 - construction preset: 1000gp +# got: '132' +# expected: '0' +not ok 37 - unnamed test +# got: '4' +# expected: 'multiple chromosomes: 4 threads' +not ok 38 - unnamed test +# got: '2' +# expected: 'multiple chromosomes: 2 contigs' +not ok 39 - unnamed test +# got: '2' +# expected: 'multiple chromosomes: 2 haplotypes' +not ok 40 - unnamed test # got: '1' +# expected: 'multiple chromosomes: 1 sample' +not ok 41 - paths as contigs with vg gbwt +# got: '132' +# expected: '0' +not ok 42 - paths as contigs with vg index +# got: '132' +# expected: '0' +not ok 43 - identical construction results with vg gbwt and vg index +# got: '2' +# expected: '0' +not ok 44 - unnamed test +# got: '2' +# expected: 'paths as contigs: 2 threads' +not ok 45 - unnamed test +# got: '2' +# expected: 'paths as contigs: 2 contigs' +not ok 46 - unnamed test +# got: '1' +# expected: 'paths as contigs: 1 haplotype' +not ok 47 - unnamed test +# got: '1' +# expected: 'paths as contigs: 1 sample' +not ok 48 - r-index construction +# got: '132' +# expected: '0' +not ok 49 - normal merging: non-empty + empty +# got: '132' +# expected: '0' +not ok 50 - the index remains unchanged +# got: '2' +# expected: '0' +not ok 51 - normal merging: empty + non-empty +# got: '132' +# expected: '0' +not ok 52 - the index remains unchanged +# got: '2' +# expected: '0' +not ok 53 - fast merging: non-empty + empty +# got: '132' +# expected: '0' +not ok 54 - the index remains unchanged +# got: '2' +# expected: '0' +not ok 55 - fast merging: empty + non-empty +# got: '132' +# expected: '0' +not ok 56 - the index remains unchanged +# got: '2' +# expected: '0' +not ok 57 - parallel merging: non-empty + empty +# got: '132' +# expected: '0' +not ok 58 - the index remains unchanged +# got: '2' +# expected: '0' +not ok 59 - parallel merging: empty + non-empty +# got: '132' +# expected: '0' +not ok 60 - the index remains unchanged +# got: '2' +# expected: '0' +not ok 61 - unnamed test +# got: '6' +# expected: 'haplotypes and paths: 6 threads' +not ok 62 - samples can be removed from a GBWT index +# got: '132' +# expected: '0' +not ok 63 - unnamed test +# got: '4' +# expected: 'haplotypes only: 4 threads' +not ok 64 - unnamed test +# got: '12' +# expected: 'all samples: 12 threads' +not ok 65 - unnamed test +# got: '6' +# expected: 'all samples: 6 haplotypes' +not ok 66 - multiple samples can be removed from a GBWT index +# got: '132' +# expected: '0' +not ok 67 - unnamed test +# got: '4' +# expected: 'sample 2: 4 threads' +not ok 68 - unnamed test +# got: '2' +# expected: 'sample 2: 2 haplotypes' +not ok 69 - threads can be extracted from GBWT +# got: '132' +# expected: '0' +not ok 70 - correct size for the thread file +# got: '0' +# expected: '121' +not ok 71 - GBWTGraph construction +# got: '132' +# expected: '0' +not ok 72 - unnamed test +# got: '8e10d978d7303ba00ceed7837fcbd793' +# expected: 'GBWTGraph was serialized correctly' +not ok 73 - GBZ construction from GBWT +# got: '132' +# expected: '0' +not ok 74 - unnamed test +# got: '472cca17cf8f139dd590e78a8a6367bb' +# expected: 'GBZ was serialized correctly' +not ok 75 - GBZ construction from VCF +# got: '132' +# expected: '0' +not ok 76 - Identical construction results from GBWT and VCF +# got: '2' +# expected: '0' +not ok 77 - GBZ construction from GBWTGraph +# got: '132' +# expected: '0' +not ok 78 - Identical construction results from XG and GBWTGraph +# got: '2' +# expected: '0' +not ok 79 - GBWT extraction from GBZ +# got: '132' +# expected: '0' +not ok 80 - Identical GBWT indexes +# got: '2' +# expected: '0' +not ok 81 - GBWT + GBWTGraph extraction from GBZ +# got: '132' +# expected: '0' +not ok 82 - Identical GBWT indexes +# got: '2' +# expected: '0' +not ok 83 - Identical GBWTGraphs +# got: '2' +# expected: '0' +not ok 84 - Path cover GBWTGraph construction +# got: '132' +# expected: '0' +not ok 85 - unnamed test +# got: '6a2738f51472e0ba1553a815a005b157' +# expected: 'GBWTGraph was serialized correctly' +not ok 86 - unnamed test +# got: '32' +# expected: 'path cover: 32 threads' +not ok 87 - unnamed test +# got: '2' +# expected: 'path cover: 2 contigs' +not ok 88 - unnamed test +# got: '16' +# expected: 'path cover: 16 haplotypes' +not ok 89 - unnamed test +# got: '16' +# expected: 'path cover: 16 samples' +not ok 90 - Path cover GBWTGraph construction +# got: '132' +# expected: '0' +not ok 91 - unnamed test +# got: '6a2738f51472e0ba1553a815a005b157' +# expected: 'GBWTGraph was serialized correctly' +not ok 92 - unnamed test +# got: '34' +# expected: 'path cover w/ paths: 34 threads' +not ok 93 - unnamed test +# got: '2' +# expected: 'path cover w/ paths: 2 contigs' +not ok 94 - unnamed test +# got: '17' +# expected: 'path cover w/ paths: 17 haplotypes' +not ok 95 - unnamed test +# got: '17' +# expected: 'path cover w/ paths: 17 samples' +not ok 96 - Local haplotypes GBWTGraph construction +# got: '132' +# expected: '0' +not ok 97 - unnamed test +# got: '00429586246711abcf1367a97d3c468c' +# expected: 'GBWTGraph was serialized correctly' +not ok 98 - unnamed test +# got: '32' +# expected: 'local haplotypes: 32 threads' +not ok 99 - unnamed test +# got: '2' +# expected: 'local haplotypes: 2 contigs' +not ok 100 - unnamed test +# got: '16' +# expected: 'local haplotypes: 16 haplotypes' +not ok 101 - unnamed test +# got: '16' +# expected: 'local haplotypes: 16 samples' +not ok 102 - Local haplotypes GBZ construction (single job) +# got: '132' +# expected: '0' +not ok 103 - unnamed test +# got: 'b6540312514c4e70aa45fc65b4bd762c' +# expected: 'GBZ was serialized correctly' +not ok 104 - Local haplotypes GBZ construction (two jobs) +# got: '132' +# expected: '0' +not ok 105 - unnamed test +# got: 'b6540312514c4e70aa45fc65b4bd762c' +# expected: 'GBZ was serialized correctly' +not ok 106 - Local haplotypes GBWTGraph construction +# got: '132' +# expected: '0' +not ok 107 - unnamed test +# got: '6a2738f51472e0ba1553a815a005b157' +# expected: 'GBWTGraph was serialized correctly' +not ok 108 - unnamed test +# got: '34' +# expected: 'local haplotypes w/ paths: 34 threads' +not ok 109 - unnamed test +# got: '2' +# expected: 'local haplotypes w/ paths: 2 contigs' +not ok 110 - unnamed test +# got: '17' +# expected: 'local haplotypes w/ paths: 17 haplotypes' +not ok 111 - unnamed test +# got: '17' +# expected: 'local haplotypes w/ paths: 17 samples' +not ok 112 - Local haplotypes with reference paths from a larger GBZ +# got: '132' +# expected: '0' +not ok 113 - unnamed test +# got: '36' +# expected: 'local haplotypes w/ paths: 36 threads' +not ok 114 - unnamed test +# got: '2' +# expected: 'local haplotypes w/ paths: 2 contigs' +not ok 115 - unnamed test +# got: '18' +# expected: 'local haplotypes w/ paths: 18 haplotypes' +not ok 116 - unnamed test +# got: '18' +# expected: 'local haplotypes w/ paths: 18 samples' +not ok 117 - local haplotypes w/ paths: reference_samples set +# got: '0' +# expected: '1' +not ok 118 - Augmented GBWTGraph construction +# got: '132' +# expected: '0' +not ok 119 - unnamed test +# got: '00429586246711abcf1367a97d3c468c' +# expected: 'GBWTGraph was serialized correctly' +not ok 120 - unnamed test +# got: '18' +# expected: 'augmented: 18 threads' +not ok 121 - unnamed test +# got: '2' +# expected: 'augmented: 2 contigs' +not ok 122 - unnamed test +# got: '18' +# expected: 'augmented: 18 haplotypes' +not ok 123 - unnamed test +# got: '17' +# expected: 'augmented: 17 samples' +not ok 124 - GBWT construction from GFA +# got: '132' +# expected: '0' +not ok 125 - unnamed test +# got: '44c27c37c7af6911c26aea2a41008460' +# expected: 'GBWT was serialized correctly' +not ok 126 - unnamed test +# got: '4' +# expected: 'gfa: 4 threads' +not ok 127 - unnamed test +# got: '2' +# expected: 'gfa: 2 contigs' +not ok 128 - unnamed test +# got: '2' +# expected: 'gfa: 2 haplotypes' +not ok 129 - unnamed test +# got: '1' +# expected: 'gfa: 1 sample' +not ok 130 - GBWT+GBWTGraph construction from GFA +# got: '132' +# expected: '0' +not ok 131 - Identical construction results with and without GBWTGraph +# got: '2' +# expected: '0' +not ok 132 - unnamed test +# got: '5c1f16564c95b54f355972f065b25b4e' +# expected: 'GBWTGraph was serialized correctly' +not ok 133 - unnamed test +# got: '0' +# expected: 'no chopping: 0 translations' +not ok 134 - GBZ construction from GFA +# got: '132' +# expected: '0' +not ok 135 - unnamed test +# got: 'ab241a3f79a781a367b701cb8888bf01' +# expected: 'GBZ was serialized correctly' +not ok 136 - GBWT+GBWTGraph construction from GFA with chopping +# got: '132' +# expected: '0' +not ok 137 - unnamed test +# got: '3' +# expected: 'chopping: 3 threads' +not ok 138 - unnamed test +# got: '1' +# expected: 'chopping: 1 contig' +not ok 139 - unnamed test +# got: '3' +# expected: 'chopping: 3 haplotypes' +not ok 140 - unnamed test +# got: '2' +# expected: 'chopping: 2 samples' +not ok 141 - unnamed test +# got: '9' +# expected: 'chopping: 9 translations' +not ok 142 - Translation can be extracted from GBZ +# got: '132' +# expected: '0' +not ok 143 - unnamed test +# got: '8' +# expected: 'from GBZ: 8 translations' +not ok 144 - GBWT+GBWTGraph construction from GFA with reference paths +# got: '132' +# expected: '0' +not ok 145 - unnamed test +# got: '6' +# expected: 'ref paths: 6 threads' +not ok 146 - unnamed test +# got: '2' +# expected: 'ref paths: 2 contigs' +not ok 147 - unnamed test +# got: '3' +# expected: 'ref paths: 3 haplotypes' +not ok 148 - unnamed test +# got: '2' +# expected: 'ref paths: 2 samples' +not ok 149 - unnamed test +# got: '0' +# expected: 'ref paths: 0 translations' +not ok 150 - GBZ construction from GFA with reference +# got: '132' +# expected: '0' +not ok 151 - GBZ GBWT tag extraction works +# got: '132' +# expected: '0' +not ok 152 - GBWT tags contain the correct reference samples +# got: '' +# expected: 'GRCh37 GRCh38' +not ok 153 - GBZ GBWT tag modification works +# got: '132' +# expected: '0' +not ok 154 - Changing reference_samples tag can make a reference a haplotype +# got: '0' +# expected: '1' +not ok 155 - Changing reference_samples tag can make a haplotype a reference +# got: '0' +# expected: '1' +not ok 156 - GBZ GBWT tag modification validation works +# got: '132' +# expected: '1' +not ok 157 - Samples can be direcly set as references +# got: '132' +# expected: '0' +not ok 158 - Direct reference assignment works +# got: '' +# expected: 'GRCh37 CHM13' +not ok 159 - GBZ can represent reference paths without haplotype numbers +# got: '0' +# expected: '2' +Failed 158/159 subtests +t/38_vg_prune.t: line 12: 3288160 Illegal instruction vg construct -m 32 -r small/xy.fa -v small/xy2.vcf.gz -R x -C -a > x.vg 2> /dev/null +t/38_vg_prune.t: line 13: 3288161 Illegal instruction vg index -G x.gbwt -v small/xy2.vcf.gz x.vg +t/38_vg_prune.t: line 16: 3288162 Illegal instruction vg prune -e 1 x.vg > y.vg +t/38_vg_prune.t: line 23: 3288169 Illegal instruction vg prune -e 1 -M 3 x.vg > y.vg +t/38_vg_prune.t: line 30: 3288176 Illegal instruction vg prune -r -e 1 x.vg > y.vg +t/38_vg_prune.t: line 37: 3288183 Illegal instruction vg prune -u -m x.mapping -g x.gbwt -e 1 x.vg > y.vg +t/38_vg_prune.t: line 44: 3288190 Illegal instruction vg prune -u -m x.mapping -e 1 x.vg > y.vg +t/38_vg_prune.t: line 54: 3288198 Illegal instruction vg construct -m 32 -r small/xy.fa -v small/xy2.vcf.gz -R x -C -a > x.vg 2> /dev/null +t/38_vg_prune.t: line 55: 3288199 Illegal instruction vg construct -m 32 -r small/xy.fa -v small/xy2.vcf.gz -R y -C -a > y.vg 2> /dev/null +t/38_vg_prune.t: line 56: 3288200 Illegal instruction vg ids -j -m xy.mapping x.vg y.vg +t/38_vg_prune.t: line 57: 3288201 Illegal instruction vg index -G x.gbwt -v small/xy2.vcf.gz x.vg +t/38_vg_prune.t: line 58: 3288202 Illegal instruction vg index -G y.gbwt -v small/xy2.vcf.gz y.vg +t/38_vg_prune.t: line 61: 3288203 Illegal instruction vg gbwt -m -o xy.gbwt x.gbwt y.gbwt +t/38_vg_prune.t: line 62: 3288204 Illegal instruction vg prune -u -m x.mapping -g xy.gbwt -e 1 x.vg > pruned.vg +head: cannot open 'xy.mapping' for reading: No such file or directory +t/38_vg_prune.t: line 69: 3288213 Illegal instruction vg prune -u -g x.gbwt -e 1 -a -m xy.mapping x.vg > /dev/null +head: cannot open 'xy.mapping' for reading: No such file or directory +t/38_vg_prune.t: line 71: 3288217 Illegal instruction vg prune -u -g y.gbwt -e 1 -a -m xy.mapping y.vg > /dev/null +head: cannot open 'xy.mapping' for reading: No such file or directory +t/38_vg_prune.t ....... +1..21 +not ok 1 - pruning produces the correct number of components +# got: '0' +# expected: '5' +not ok 2 - unnamed test +# got: '51' +# expected: 'pruning leaves the correct number of nodes' +not ok 3 - unnamed test +# got: '51' +# expected: 'pruning leaves the correct number of edges' +not ok 4 - pruning without high-degree nodes produces the correct number of components +# got: '0' +# expected: '6' +not ok 5 - unnamed test +# got: '50' +# expected: 'pruning without high-degree nodes leaves the correct number of nodes' +not ok 6 - unnamed test +# got: '47' +# expected: 'pruning without high-degree nodes leaves the correct number of edges' +not ok 7 - pruning with path restoring produces the correct number of components +# got: '0' +# expected: '1' +not ok 8 - unnamed test +# got: '64' +# expected: 'pruning with path restoring leaves the correct number of nodes' +not ok 9 - unnamed test +# got: '68' +# expected: 'pruning with path restoring leaves the correct number of edges' +not ok 10 - pruning with path/thread unfolding produces the correct number of components +# got: '0' +# expected: '1' +not ok 11 - unnamed test +# got: '80' +# expected: 'pruning with path/thread unfolding produces the correct number of nodes' +not ok 12 - unnamed test +# got: '92' +# expected: 'pruning with path/thread unfolding produces the correct number of edges' +not ok 13 - pruning with path unfolding produces the correct number of components +# got: '0' +# expected: '1' +not ok 14 - unnamed test +# got: '64' +# expected: 'pruning with path unfolding produces the correct number of nodes' +not ok 15 - unnamed test +# got: '68' +# expected: 'pruning with path unfolding produces the correct number of edges' +not ok 16 - unfolding with multi-chromosome GBWT produces the correct number of components +# got: '0' +# expected: '1' +not ok 17 - unnamed test +# got: '80' +# expected: 'unfolding with multi-chromosome GBWT produces the correct number of nodes' +not ok 18 - unnamed test +# got: '92' +# expected: 'unfolding with multi-chromosome GBWT produces the correct number of edges' +not ok 19 - unnamed test +# got: '139_0_139_0_' +# expected: 'empty mapping starts from the right node id' +not ok 20 - unnamed test +# got: '139_0_168_0_' +# expected: 'the first unfolded graph adds the correct number of nodes to the mapping' +not ok 21 - unnamed test +# got: '139_0_196_0_' +# expected: 'the second unfolded graph adds the correct number of nodes to the mapping' +Failed 21/21 subtests +t/39_vg_inject.t: line 11: 3288225 Illegal instruction vg construct -r small/x.fa > j.vg +t/39_vg_inject.t: line 12: 3288226 Illegal instruction vg index -x j.xg j.vg +t/39_vg_inject.t: line 13: 3288227 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > x.vg +t/39_vg_inject.t: line 14: 3288228 Illegal instruction vg index -k 11 -g x.gcsa -x x.xg x.vg +[main_samview] fail to read the header from "-". +[main_samview] fail to read the header from "-". +[main_samview] fail to read the header from "-". +[main_samview] fail to read the header from "-". +[main_samview] fail to read the header from "-". +[main_samview] fail to read the header from "-". +rm: cannot remove 'j.xg': No such file or directory +rm: cannot remove 'x.gcsa': No such file or directory +rm: cannot remove 'x.gcsa.lcp': No such file or directory +rm: cannot remove 'x.xg': No such file or directory +t/39_vg_inject.t ...... +1..14 +not ok 1 - reads are generated +# got: '0' +# expected: '1000' +not ok 2 - vg inject works for all reads included in the original bam +# got: '0' +# expected: '1000' +not ok 3 - vg inject retains read names +# got: 'small/x.fa.fastq.000000000 +# small/x.fa.fastq.000000001 +# small/x.fa.fastq.000000002 +# small/x.fa.fastq.000000003 +# small/x.fa.fastq.000000004 +# small/x.fa.fastq.000000005 +# small/x.fa.fastq.000000006 +# small/x.fa.fastq.000000007 +# small/x.fa.fastq.000000008 +# small/x.fa.fastq.000000009 +# small/x.fa.fastq.000000010 +# small/x.fa.fastq.000000011 +# small/x.fa.fastq.000000012 +# small/x.fa.fastq.000000013 +# small/x.fa.fastq.000000014 +# small/x.fa.fastq.000000015 +# small/x.fa.fastq.000000016 +# small/x.fa.fastq.000000017 +# small/x.fa.fastq.000000018 +# small/x.fa.fastq.000000019 +# small/x.fa.fastq.000000020 +# small/x.fa.fastq.000000021 +# small/x.fa.fastq.000000022 +# small/x.fa.fastq.000000023 +# small/x.fa.fastq.000000024 +# small/x.fa.fastq.000000025 +# small/x.fa.fastq.000000026 +# small/x.fa.fastq.000000027 +# small/x.fa.fastq.000000028 +# small/x.fa.fastq.000000029 +# small/x.fa.fastq.000000030 +# small/x.fa.fastq.000000031 +# small/x.fa.fastq.000000032 +# small/x.fa.fastq.000000033 +# small/x.fa.fastq.000000034 +# small/x.fa.fastq.000000035 +# small/x.fa.fastq.000000036 +# small/x.fa.fastq.000000037 +# small/x.fa.fastq.000000038 +# small/x.fa.fastq.000000039 +# small/x.fa.fastq.000000040 +# small/x.fa.fastq.000000041 +# small/x.fa.fastq.000000042 +# small/x.fa.fastq.000000043 +# small/x.fa.fastq.000000044 +# small/x.fa.fastq.000000045 +# small/x.fa.fastq.000000046 +# small/x.fa.fastq.000000047 +# small/x.fa.fastq.000000048 +# small/x.fa.fastq.000000049 +# small/x.fa.fastq.000000050 +# small/x.fa.fastq.000000051 +# small/x.fa.fastq.000000052 +# small/x.fa.fastq.000000053 +# small/x.fa.fastq.000000054 +# small/x.fa.fastq.000000055 +# small/x.fa.fastq.000000056 +# small/x.fa.fastq.000000057 +# small/x.fa.fastq.000000058 +# small/x.fa.fastq.000000059 +# small/x.fa.fastq.000000060 +# small/x.fa.fastq.000000061 +# small/x.fa.fastq.000000062 +# small/x.fa.fastq.000000063 +# small/x.fa.fastq.000000064 +# small/x.fa.fastq.000000065 +# small/x.fa.fastq.000000066 +# small/x.fa.fastq.000000067 +# small/x.fa.fastq.000000068 +# small/x.fa.fastq.000000069 +# small/x.fa.fastq.000000070 +# small/x.fa.fastq.000000071 +# small/x.fa.fastq.000000072 +# small/x.fa.fastq.000000073 +# small/x.fa.fastq.000000074 +# small/x.fa.fastq.000000075 +# small/x.fa.fastq.000000076 +# small/x.fa.fastq.000000077 +# small/x.fa.fastq.000000078 +# small/x.fa.fastq.000000079 +# small/x.fa.fastq.000000080 +# small/x.fa.fastq.000000081 +# small/x.fa.fastq.000000082 +# small/x.fa.fastq.000000083 +# small/x.fa.fastq.000000084 +# small/x.fa.fastq.000000085 +# small/x.fa.fastq.000000086 +# small/x.fa.fastq.000000087 +# small/x.fa.fastq.000000088 +# small/x.fa.fastq.000000089 +# small/x.fa.fastq.000000090 +# small/x.fa.fastq.000000091 +# small/x.fa.fastq.000000092 +# small/x.fa.fastq.000000093 +# small/x.fa.fastq.000000094 +# small/x.fa.fastq.000000095 +# small/x.fa.fastq.000000096 +# small/x.fa.fastq.000000097 +# small/x.fa.fastq.000000098 +# small/x.fa.fastq.000000099 +# small/x.fa.fastq.000000100 +# small/x.fa.fastq.000000101 +# small/x.fa.fastq.000000102 +# small/x.fa.fastq.000000103 +# small/x.fa.fastq.000000104 +# small/x.fa.fastq.000000105 +# small/x.fa.fastq.000000106 +# small/x.fa.fastq.000000107 +# small/x.fa.fastq.000000108 +# small/x.fa.fastq.000000109 +# small/x.fa.fastq.000000110 +# small/x.fa.fastq.000000111 +# small/x.fa.fastq.000000112 +# small/x.fa.fastq.000000113 +# small/x.fa.fastq.000000114 +# small/x.fa.fastq.000000115 +# small/x.fa.fastq.000000116 +# small/x.fa.fastq.000000117 +# small/x.fa.fastq.000000118 +# small/x.fa.fastq.000000119 +# small/x.fa.fastq.000000120 +# small/x.fa.fastq.000000121 +# small/x.fa.fastq.000000122 +# small/x.fa.fastq.000000123 +# small/x.fa.fastq.000000124 +# small/x.fa.fastq.000000125 +# small/x.fa.fastq.000000126 +# small/x.fa.fastq.000000127 +# small/x.fa.fastq.000000128 +# small/x.fa.fastq.000000129 +# small/x.fa.fastq.000000130 +# small/x.fa.fastq.000000131 +# small/x.fa.fastq.000000132 +# small/x.fa.fastq.000000133 +# small/x.fa.fastq.000000134 +# small/x.fa.fastq.000000135 +# small/x.fa.fastq.000000136 +# small/x.fa.fastq.000000137 +# small/x.fa.fastq.000000138 +# small/x.fa.fastq.000000139 +# small/x.fa.fastq.000000140 +# small/x.fa.fastq.000000141 +# small/x.fa.fastq.000000142 +# small/x.fa.fastq.000000143 +# small/x.fa.fastq.000000144 +# small/x.fa.fastq.000000145 +# small/x.fa.fastq.000000146 +# small/x.fa.fastq.000000147 +# small/x.fa.fastq.000000148 +# small/x.fa.fastq.000000149 +# small/x.fa.fastq.000000150 +# small/x.fa.fastq.000000151 +# small/x.fa.fastq.000000152 +# small/x.fa.fastq.000000153 +# small/x.fa.fastq.000000154 +# small/x.fa.fastq.000000155 +# small/x.fa.fastq.000000156 +# small/x.fa.fastq.000000157 +# small/x.fa.fastq.000000158 +# small/x.fa.fastq.000000159 +# small/x.fa.fastq.000000160 +# small/x.fa.fastq.000000161 +# small/x.fa.fastq.000000162 +# small/x.fa.fastq.000000163 +# small/x.fa.fastq.000000164 +# small/x.fa.fastq.000000165 +# small/x.fa.fastq.000000166 +# small/x.fa.fastq.000000167 +# small/x.fa.fastq.000000168 +# small/x.fa.fastq.000000169 +# small/x.fa.fastq.000000170 +# small/x.fa.fastq.000000171 +# small/x.fa.fastq.000000172 +# small/x.fa.fastq.000000173 +# small/x.fa.fastq.000000174 +# small/x.fa.fastq.000000175 +# small/x.fa.fastq.000000176 +# small/x.fa.fastq.000000177 +# small/x.fa.fastq.000000178 +# small/x.fa.fastq.000000179 +# small/x.fa.fastq.000000180 +# small/x.fa.fastq.000000181 +# small/x.fa.fastq.000000182 +# small/x.fa.fastq.000000183 +# small/x.fa.fastq.000000184 +# small/x.fa.fastq.000000185 +# small/x.fa.fastq.000000186 +# small/x.fa.fastq.000000187 +# small/x.fa.fastq.000000188 +# small/x.fa.fastq.000000189 +# small/x.fa.fastq.000000190 +# small/x.fa.fastq.000000191 +# small/x.fa.fastq.000000192 +# small/x.fa.fastq.000000193 +# small/x.fa.fastq.000000194 +# small/x.fa.fastq.000000195 +# small/x.fa.fastq.000000196 +# small/x.fa.fastq.000000197 +# small/x.fa.fastq.000000198 +# small/x.fa.fastq.000000199 +# small/x.fa.fastq.000000200 +# small/x.fa.fastq.000000201 +# small/x.fa.fastq.000000202 +# small/x.fa.fastq.000000203 +# small/x.fa.fastq.000000204 +# small/x.fa.fastq.000000205 +# small/x.fa.fastq.000000206 +# small/x.fa.fastq.000000207 +# small/x.fa.fastq.000000208 +# small/x.fa.fastq.000000209 +# small/x.fa.fastq.000000210 +# small/x.fa.fastq.000000211 +# small/x.fa.fastq.000000212 +# small/x.fa.fastq.000000213 +# small/x.fa.fastq.000000214 +# small/x.fa.fastq.000000215 +# small/x.fa.fastq.000000216 +# small/x.fa.fastq.000000217 +# small/x.fa.fastq.000000218 +# small/x.fa.fastq.000000219 +# small/x.fa.fastq.000000220 +# small/x.fa.fastq.000000221 +# small/x.fa.fastq.000000222 +# small/x.fa.fastq.000000223 +# small/x.fa.fastq.000000224 +# small/x.fa.fastq.000000225 +# small/x.fa.fastq.000000226 +# small/x.fa.fastq.000000227 +# small/x.fa.fastq.000000228 +# small/x.fa.fastq.000000229 +# small/x.fa.fastq.000000230 +# small/x.fa.fastq.000000231 +# small/x.fa.fastq.000000232 +# small/x.fa.fastq.000000233 +# small/x.fa.fastq.000000234 +# small/x.fa.fastq.000000235 +# small/x.fa.fastq.000000236 +# small/x.fa.fastq.000000237 +# small/x.fa.fastq.000000238 +# small/x.fa.fastq.000000239 +# small/x.fa.fastq.000000240 +# small/x.fa.fastq.000000241 +# small/x.fa.fastq.000000242 +# small/x.fa.fastq.000000243 +# small/x.fa.fastq.000000244 +# small/x.fa.fastq.000000245 +# small/x.fa.fastq.000000246 +# small/x.fa.fastq.000000247 +# small/x.fa.fastq.000000248 +# small/x.fa.fastq.000000249 +# small/x.fa.fastq.000000250 +# small/x.fa.fastq.000000251 +# small/x.fa.fastq.000000252 +# small/x.fa.fastq.000000253 +# small/x.fa.fastq.000000254 +# small/x.fa.fastq.000000255 +# small/x.fa.fastq.000000256 +# small/x.fa.fastq.000000257 +# small/x.fa.fastq.000000258 +# small/x.fa.fastq.000000259 +# small/x.fa.fastq.000000260 +# small/x.fa.fastq.000000261 +# small/x.fa.fastq.000000262 +# small/x.fa.fastq.000000263 +# small/x.fa.fastq.000000264 +# small/x.fa.fastq.000000265 +# small/x.fa.fastq.000000266 +# small/x.fa.fastq.000000267 +# small/x.fa.fastq.000000268 +# small/x.fa.fastq.000000269 +# small/x.fa.fastq.000000270 +# small/x.fa.fastq.000000271 +# small/x.fa.fastq.000000272 +# small/x.fa.fastq.000000273 +# small/x.fa.fastq.000000274 +# small/x.fa.fastq.000000275 +# small/x.fa.fastq.000000276 +# small/x.fa.fastq.000000277 +# small/x.fa.fastq.000000278 +# small/x.fa.fastq.000000279 +# small/x.fa.fastq.000000280 +# small/x.fa.fastq.000000281 +# small/x.fa.fastq.000000282 +# small/x.fa.fastq.000000283 +# small/x.fa.fastq.000000284 +# small/x.fa.fastq.000000285 +# small/x.fa.fastq.000000286 +# small/x.fa.fastq.000000287 +# small/x.fa.fastq.000000288 +# small/x.fa.fastq.000000289 +# small/x.fa.fastq.000000290 +# small/x.fa.fastq.000000291 +# small/x.fa.fastq.000000292 +# small/x.fa.fastq.000000293 +# small/x.fa.fastq.000000294 +# small/x.fa.fastq.000000295 +# small/x.fa.fastq.000000296 +# small/x.fa.fastq.000000297 +# small/x.fa.fastq.000000298 +# small/x.fa.fastq.000000299 +# small/x.fa.fastq.000000300 +# small/x.fa.fastq.000000301 +# small/x.fa.fastq.000000302 +# small/x.fa.fastq.000000303 +# small/x.fa.fastq.000000304 +# small/x.fa.fastq.000000305 +# small/x.fa.fastq.000000306 +# small/x.fa.fastq.000000307 +# small/x.fa.fastq.000000308 +# small/x.fa.fastq.000000309 +# small/x.fa.fastq.000000310 +# small/x.fa.fastq.000000311 +# small/x.fa.fastq.000000312 +# small/x.fa.fastq.000000313 +# small/x.fa.fastq.000000314 +# small/x.fa.fastq.000000315 +# small/x.fa.fastq.000000316 +# small/x.fa.fastq.000000317 +# small/x.fa.fastq.000000318 +# small/x.fa.fastq.000000319 +# small/x.fa.fastq.000000320 +# small/x.fa.fastq.000000321 +# small/x.fa.fastq.000000322 +# small/x.fa.fastq.000000323 +# small/x.fa.fastq.000000324 +# small/x.fa.fastq.000000325 +# small/x.fa.fastq.000000326 +# small/x.fa.fastq.000000327 +# small/x.fa.fastq.000000328 +# small/x.fa.fastq.000000329 +# small/x.fa.fastq.000000330 +# small/x.fa.fastq.000000331 +# small/x.fa.fastq.000000332 +# small/x.fa.fastq.000000333 +# small/x.fa.fastq.000000334 +# small/x.fa.fastq.000000335 +# small/x.fa.fastq.000000336 +# small/x.fa.fastq.000000337 +# small/x.fa.fastq.000000338 +# small/x.fa.fastq.000000339 +# small/x.fa.fastq.000000340 +# small/x.fa.fastq.000000341 +# small/x.fa.fastq.000000342 +# small/x.fa.fastq.000000343 +# small/x.fa.fastq.000000344 +# small/x.fa.fastq.000000345 +# small/x.fa.fastq.000000346 +# small/x.fa.fastq.000000347 +# small/x.fa.fastq.000000348 +# small/x.fa.fastq.000000349 +# small/x.fa.fastq.000000350 +# small/x.fa.fastq.000000351 +# small/x.fa.fastq.000000352 +# small/x.fa.fastq.000000353 +# small/x.fa.fastq.000000354 +# small/x.fa.fastq.000000355 +# small/x.fa.fastq.000000356 +# small/x.fa.fastq.000000357 +# small/x.fa.fastq.000000358 +# small/x.fa.fastq.000000359 +# small/x.fa.fastq.000000360 +# small/x.fa.fastq.000000361 +# small/x.fa.fastq.000000362 +# small/x.fa.fastq.000000363 +# small/x.fa.fastq.000000364 +# small/x.fa.fastq.000000365 +# small/x.fa.fastq.000000366 +# small/x.fa.fastq.000000367 +# small/x.fa.fastq.000000368 +# small/x.fa.fastq.000000369 +# small/x.fa.fastq.000000370 +# small/x.fa.fastq.000000371 +# small/x.fa.fastq.000000372 +# small/x.fa.fastq.000000373 +# small/x.fa.fastq.000000374 +# small/x.fa.fastq.000000375 +# small/x.fa.fastq.000000376 +# small/x.fa.fastq.000000377 +# small/x.fa.fastq.000000378 +# small/x.fa.fastq.000000379 +# small/x.fa.fastq.000000380 +# small/x.fa.fastq.000000381 +# small/x.fa.fastq.000000382 +# small/x.fa.fastq.000000383 +# small/x.fa.fastq.000000384 +# small/x.fa.fastq.000000385 +# small/x.fa.fastq.000000386 +# small/x.fa.fastq.000000387 +# small/x.fa.fastq.000000388 +# small/x.fa.fastq.000000389 +# small/x.fa.fastq.000000390 +# small/x.fa.fastq.000000391 +# small/x.fa.fastq.000000392 +# small/x.fa.fastq.000000393 +# small/x.fa.fastq.000000394 +# small/x.fa.fastq.000000395 +# small/x.fa.fastq.000000396 +# small/x.fa.fastq.000000397 +# small/x.fa.fastq.000000398 +# small/x.fa.fastq.000000399 +# small/x.fa.fastq.000000400 +# small/x.fa.fastq.000000401 +# small/x.fa.fastq.000000402 +# small/x.fa.fastq.000000403 +# small/x.fa.fastq.000000404 +# small/x.fa.fastq.000000405 +# small/x.fa.fastq.000000406 +# small/x.fa.fastq.000000407 +# small/x.fa.fastq.000000408 +# small/x.fa.fastq.000000409 +# small/x.fa.fastq.000000410 +# small/x.fa.fastq.000000411 +# small/x.fa.fastq.000000412 +# small/x.fa.fastq.000000413 +# small/x.fa.fastq.000000414 +# small/x.fa.fastq.000000415 +# small/x.fa.fastq.000000416 +# small/x.fa.fastq.000000417 +# small/x.fa.fastq.000000418 +# small/x.fa.fastq.000000419 +# small/x.fa.fastq.000000420 +# small/x.fa.fastq.000000421 +# small/x.fa.fastq.000000422 +# small/x.fa.fastq.000000423 +# small/x.fa.fastq.000000424 +# small/x.fa.fastq.000000425 +# small/x.fa.fastq.000000426 +# small/x.fa.fastq.000000427 +# small/x.fa.fastq.000000428 +# small/x.fa.fastq.000000429 +# small/x.fa.fastq.000000430 +# small/x.fa.fastq.000000431 +# small/x.fa.fastq.000000432 +# small/x.fa.fastq.000000433 +# small/x.fa.fastq.000000434 +# small/x.fa.fastq.000000435 +# small/x.fa.fastq.000000436 +# small/x.fa.fastq.000000437 +# small/x.fa.fastq.000000438 +# small/x.fa.fastq.000000439 +# small/x.fa.fastq.000000440 +# small/x.fa.fastq.000000441 +# small/x.fa.fastq.000000442 +# small/x.fa.fastq.000000443 +# small/x.fa.fastq.000000444 +# small/x.fa.fastq.000000445 +# small/x.fa.fastq.000000446 +# small/x.fa.fastq.000000447 +# small/x.fa.fastq.000000448 +# small/x.fa.fastq.000000449 +# small/x.fa.fastq.000000450 +# small/x.fa.fastq.000000451 +# small/x.fa.fastq.000000452 +# small/x.fa.fastq.000000453 +# small/x.fa.fastq.000000454 +# small/x.fa.fastq.000000455 +# small/x.fa.fastq.000000456 +# small/x.fa.fastq.000000457 +# small/x.fa.fastq.000000458 +# small/x.fa.fastq.000000459 +# small/x.fa.fastq.000000460 +# small/x.fa.fastq.000000461 +# small/x.fa.fastq.000000462 +# small/x.fa.fastq.000000463 +# small/x.fa.fastq.000000464 +# small/x.fa.fastq.000000465 +# small/x.fa.fastq.000000466 +# small/x.fa.fastq.000000467 +# small/x.fa.fastq.000000468 +# small/x.fa.fastq.000000469 +# small/x.fa.fastq.000000470 +# small/x.fa.fastq.000000471 +# small/x.fa.fastq.000000472 +# small/x.fa.fastq.000000473 +# small/x.fa.fastq.000000474 +# small/x.fa.fastq.000000475 +# small/x.fa.fastq.000000476 +# small/x.fa.fastq.000000477 +# small/x.fa.fastq.000000478 +# small/x.fa.fastq.000000479 +# small/x.fa.fastq.000000480 +# small/x.fa.fastq.000000481 +# small/x.fa.fastq.000000482 +# small/x.fa.fastq.000000483 +# small/x.fa.fastq.000000484 +# small/x.fa.fastq.000000485 +# small/x.fa.fastq.000000486 +# small/x.fa.fastq.000000487 +# small/x.fa.fastq.000000488 +# small/x.fa.fastq.000000489 +# small/x.fa.fastq.000000490 +# small/x.fa.fastq.000000491 +# small/x.fa.fastq.000000492 +# small/x.fa.fastq.000000493 +# small/x.fa.fastq.000000494 +# small/x.fa.fastq.000000495 +# small/x.fa.fastq.000000496 +# small/x.fa.fastq.000000497 +# small/x.fa.fastq.000000498 +# small/x.fa.fastq.000000499 +# small/x.fa.fastq.000000500 +# small/x.fa.fastq.000000501 +# small/x.fa.fastq.000000502 +# small/x.fa.fastq.000000503 +# small/x.fa.fastq.000000504 +# small/x.fa.fastq.000000505 +# small/x.fa.fastq.000000506 +# small/x.fa.fastq.000000507 +# small/x.fa.fastq.000000508 +# small/x.fa.fastq.000000509 +# small/x.fa.fastq.000000510 +# small/x.fa.fastq.000000511 +# small/x.fa.fastq.000000512 +# small/x.fa.fastq.000000513 +# small/x.fa.fastq.000000514 +# small/x.fa.fastq.000000515 +# small/x.fa.fastq.000000516 +# small/x.fa.fastq.000000517 +# small/x.fa.fastq.000000518 +# small/x.fa.fastq.000000519 +# small/x.fa.fastq.000000520 +# small/x.fa.fastq.000000521 +# small/x.fa.fastq.000000522 +# small/x.fa.fastq.000000523 +# small/x.fa.fastq.000000524 +# small/x.fa.fastq.000000525 +# small/x.fa.fastq.000000526 +# small/x.fa.fastq.000000527 +# small/x.fa.fastq.000000528 +# small/x.fa.fastq.000000529 +# small/x.fa.fastq.000000530 +# small/x.fa.fastq.000000531 +# small/x.fa.fastq.000000532 +# small/x.fa.fastq.000000533 +# small/x.fa.fastq.000000534 +# small/x.fa.fastq.000000535 +# small/x.fa.fastq.000000536 +# small/x.fa.fastq.000000537 +# small/x.fa.fastq.000000538 +# small/x.fa.fastq.000000539 +# small/x.fa.fastq.000000540 +# small/x.fa.fastq.000000541 +# small/x.fa.fastq.000000542 +# small/x.fa.fastq.000000543 +# small/x.fa.fastq.000000544 +# small/x.fa.fastq.000000545 +# small/x.fa.fastq.000000546 +# small/x.fa.fastq.000000547 +# small/x.fa.fastq.000000548 +# small/x.fa.fastq.000000549 +# small/x.fa.fastq.000000550 +# small/x.fa.fastq.000000551 +# small/x.fa.fastq.000000552 +# small/x.fa.fastq.000000553 +# small/x.fa.fastq.000000554 +# small/x.fa.fastq.000000555 +# small/x.fa.fastq.000000556 +# small/x.fa.fastq.000000557 +# small/x.fa.fastq.000000558 +# small/x.fa.fastq.000000559 +# small/x.fa.fastq.000000560 +# small/x.fa.fastq.000000561 +# small/x.fa.fastq.000000562 +# small/x.fa.fastq.000000563 +# small/x.fa.fastq.000000564 +# small/x.fa.fastq.000000565 +# small/x.fa.fastq.000000566 +# small/x.fa.fastq.000000567 +# small/x.fa.fastq.000000568 +# small/x.fa.fastq.000000569 +# small/x.fa.fastq.000000570 +# small/x.fa.fastq.000000571 +# small/x.fa.fastq.000000572 +# small/x.fa.fastq.000000573 +# small/x.fa.fastq.000000574 +# small/x.fa.fastq.000000575 +# small/x.fa.fastq.000000576 +# small/x.fa.fastq.000000577 +# small/x.fa.fastq.000000578 +# small/x.fa.fastq.000000579 +# small/x.fa.fastq.000000580 +# small/x.fa.fastq.000000581 +# small/x.fa.fastq.000000582 +# small/x.fa.fastq.000000583 +# small/x.fa.fastq.000000584 +# small/x.fa.fastq.000000585 +# small/x.fa.fastq.000000586 +# small/x.fa.fastq.000000587 +# small/x.fa.fastq.000000588 +# small/x.fa.fastq.000000589 +# small/x.fa.fastq.000000590 +# small/x.fa.fastq.000000591 +# small/x.fa.fastq.000000592 +# small/x.fa.fastq.000000593 +# small/x.fa.fastq.000000594 +# small/x.fa.fastq.000000595 +# small/x.fa.fastq.000000596 +# small/x.fa.fastq.000000597 +# small/x.fa.fastq.000000598 +# small/x.fa.fastq.000000599 +# small/x.fa.fastq.000000600 +# small/x.fa.fastq.000000601 +# small/x.fa.fastq.000000602 +# small/x.fa.fastq.000000603 +# small/x.fa.fastq.000000604 +# small/x.fa.fastq.000000605 +# small/x.fa.fastq.000000606 +# small/x.fa.fastq.000000607 +# small/x.fa.fastq.000000608 +# small/x.fa.fastq.000000609 +# small/x.fa.fastq.000000610 +# small/x.fa.fastq.000000611 +# small/x.fa.fastq.000000612 +# small/x.fa.fastq.000000613 +# small/x.fa.fastq.000000614 +# small/x.fa.fastq.000000615 +# small/x.fa.fastq.000000616 +# small/x.fa.fastq.000000617 +# small/x.fa.fastq.000000618 +# small/x.fa.fastq.000000619 +# small/x.fa.fastq.000000620 +# small/x.fa.fastq.000000621 +# small/x.fa.fastq.000000622 +# small/x.fa.fastq.000000623 +# small/x.fa.fastq.000000624 +# small/x.fa.fastq.000000625 +# small/x.fa.fastq.000000626 +# small/x.fa.fastq.000000627 +# small/x.fa.fastq.000000628 +# small/x.fa.fastq.000000629 +# small/x.fa.fastq.000000630 +# small/x.fa.fastq.000000631 +# small/x.fa.fastq.000000632 +# small/x.fa.fastq.000000633 +# small/x.fa.fastq.000000634 +# small/x.fa.fastq.000000635 +# small/x.fa.fastq.000000636 +# small/x.fa.fastq.000000637 +# small/x.fa.fastq.000000638 +# small/x.fa.fastq.000000639 +# small/x.fa.fastq.000000640 +# small/x.fa.fastq.000000641 +# small/x.fa.fastq.000000642 +# small/x.fa.fastq.000000643 +# small/x.fa.fastq.000000644 +# small/x.fa.fastq.000000645 +# small/x.fa.fastq.000000646 +# small/x.fa.fastq.000000647 +# small/x.fa.fastq.000000648 +# small/x.fa.fastq.000000649 +# small/x.fa.fastq.000000650 +# small/x.fa.fastq.000000651 +# small/x.fa.fastq.000000652 +# small/x.fa.fastq.000000653 +# small/x.fa.fastq.000000654 +# small/x.fa.fastq.000000655 +# small/x.fa.fastq.000000656 +# small/x.fa.fastq.000000657 +# small/x.fa.fastq.000000658 +# small/x.fa.fastq.000000659 +# small/x.fa.fastq.000000660 +# small/x.fa.fastq.000000661 +# small/x.fa.fastq.000000662 +# small/x.fa.fastq.000000663 +# small/x.fa.fastq.000000664 +# small/x.fa.fastq.000000665 +# small/x.fa.fastq.000000666 +# small/x.fa.fastq.000000667 +# small/x.fa.fastq.000000668 +# small/x.fa.fastq.000000669 +# small/x.fa.fastq.000000670 +# small/x.fa.fastq.000000671 +# small/x.fa.fastq.000000672 +# small/x.fa.fastq.000000673 +# small/x.fa.fastq.000000674 +# small/x.fa.fastq.000000675 +# small/x.fa.fastq.000000676 +# small/x.fa.fastq.000000677 +# small/x.fa.fastq.000000678 +# small/x.fa.fastq.000000679 +# small/x.fa.fastq.000000680 +# small/x.fa.fastq.000000681 +# small/x.fa.fastq.000000682 +# small/x.fa.fastq.000000683 +# small/x.fa.fastq.000000684 +# small/x.fa.fastq.000000685 +# small/x.fa.fastq.000000686 +# small/x.fa.fastq.000000687 +# small/x.fa.fastq.000000688 +# small/x.fa.fastq.000000689 +# small/x.fa.fastq.000000690 +# small/x.fa.fastq.000000691 +# small/x.fa.fastq.000000692 +# small/x.fa.fastq.000000693 +# small/x.fa.fastq.000000694 +# small/x.fa.fastq.000000695 +# small/x.fa.fastq.000000696 +# small/x.fa.fastq.000000697 +# small/x.fa.fastq.000000698 +# small/x.fa.fastq.000000699 +# small/x.fa.fastq.000000700 +# small/x.fa.fastq.000000701 +# small/x.fa.fastq.000000702 +# small/x.fa.fastq.000000703 +# small/x.fa.fastq.000000704 +# small/x.fa.fastq.000000705 +# small/x.fa.fastq.000000706 +# small/x.fa.fastq.000000707 +# small/x.fa.fastq.000000708 +# small/x.fa.fastq.000000709 +# small/x.fa.fastq.000000710 +# small/x.fa.fastq.000000711 +# small/x.fa.fastq.000000712 +# small/x.fa.fastq.000000713 +# small/x.fa.fastq.000000714 +# small/x.fa.fastq.000000715 +# small/x.fa.fastq.000000716 +# small/x.fa.fastq.000000717 +# small/x.fa.fastq.000000718 +# small/x.fa.fastq.000000719 +# small/x.fa.fastq.000000720 +# small/x.fa.fastq.000000721 +# small/x.fa.fastq.000000722 +# small/x.fa.fastq.000000723 +# small/x.fa.fastq.000000724 +# small/x.fa.fastq.000000725 +# small/x.fa.fastq.000000726 +# small/x.fa.fastq.000000727 +# small/x.fa.fastq.000000728 +# small/x.fa.fastq.000000729 +# small/x.fa.fastq.000000730 +# small/x.fa.fastq.000000731 +# small/x.fa.fastq.000000732 +# small/x.fa.fastq.000000733 +# small/x.fa.fastq.000000734 +# small/x.fa.fastq.000000735 +# small/x.fa.fastq.000000736 +# small/x.fa.fastq.000000737 +# small/x.fa.fastq.000000738 +# small/x.fa.fastq.000000739 +# small/x.fa.fastq.000000740 +# small/x.fa.fastq.000000741 +# small/x.fa.fastq.000000742 +# small/x.fa.fastq.000000743 +# small/x.fa.fastq.000000744 +# small/x.fa.fastq.000000745 +# small/x.fa.fastq.000000746 +# small/x.fa.fastq.000000747 +# small/x.fa.fastq.000000748 +# small/x.fa.fastq.000000749 +# small/x.fa.fastq.000000750 +# small/x.fa.fastq.000000751 +# small/x.fa.fastq.000000752 +# small/x.fa.fastq.000000753 +# small/x.fa.fastq.000000754 +# small/x.fa.fastq.000000755 +# small/x.fa.fastq.000000756 +# small/x.fa.fastq.000000757 +# small/x.fa.fastq.000000758 +# small/x.fa.fastq.000000759 +# small/x.fa.fastq.000000760 +# small/x.fa.fastq.000000761 +# small/x.fa.fastq.000000762 +# small/x.fa.fastq.000000763 +# small/x.fa.fastq.000000764 +# small/x.fa.fastq.000000765 +# small/x.fa.fastq.000000766 +# small/x.fa.fastq.000000767 +# small/x.fa.fastq.000000768 +# small/x.fa.fastq.000000769 +# small/x.fa.fastq.000000770 +# small/x.fa.fastq.000000771 +# small/x.fa.fastq.000000772 +# small/x.fa.fastq.000000773 +# small/x.fa.fastq.000000774 +# small/x.fa.fastq.000000775 +# small/x.fa.fastq.000000776 +# small/x.fa.fastq.000000777 +# small/x.fa.fastq.000000778 +# small/x.fa.fastq.000000779 +# small/x.fa.fastq.000000780 +# small/x.fa.fastq.000000781 +# small/x.fa.fastq.000000782 +# small/x.fa.fastq.000000783 +# small/x.fa.fastq.000000784 +# small/x.fa.fastq.000000785 +# small/x.fa.fastq.000000786 +# small/x.fa.fastq.000000787 +# small/x.fa.fastq.000000788 +# small/x.fa.fastq.000000789 +# small/x.fa.fastq.000000790 +# small/x.fa.fastq.000000791 +# small/x.fa.fastq.000000792 +# small/x.fa.fastq.000000793 +# small/x.fa.fastq.000000794 +# small/x.fa.fastq.000000795 +# small/x.fa.fastq.000000796 +# small/x.fa.fastq.000000797 +# small/x.fa.fastq.000000798 +# small/x.fa.fastq.000000799 +# small/x.fa.fastq.000000800 +# small/x.fa.fastq.000000801 +# small/x.fa.fastq.000000802 +# small/x.fa.fastq.000000803 +# small/x.fa.fastq.000000804 +# small/x.fa.fastq.000000805 +# small/x.fa.fastq.000000806 +# small/x.fa.fastq.000000807 +# small/x.fa.fastq.000000808 +# small/x.fa.fastq.000000809 +# small/x.fa.fastq.000000810 +# small/x.fa.fastq.000000811 +# small/x.fa.fastq.000000812 +# small/x.fa.fastq.000000813 +# small/x.fa.fastq.000000814 +# small/x.fa.fastq.000000815 +# small/x.fa.fastq.000000816 +# small/x.fa.fastq.000000817 +# small/x.fa.fastq.000000818 +# small/x.fa.fastq.000000819 +# small/x.fa.fastq.000000820 +# small/x.fa.fastq.000000821 +# small/x.fa.fastq.000000822 +# small/x.fa.fastq.000000823 +# small/x.fa.fastq.000000824 +# small/x.fa.fastq.000000825 +# small/x.fa.fastq.000000826 +# small/x.fa.fastq.000000827 +# small/x.fa.fastq.000000828 +# small/x.fa.fastq.000000829 +# small/x.fa.fastq.000000830 +# small/x.fa.fastq.000000831 +# small/x.fa.fastq.000000832 +# small/x.fa.fastq.000000833 +# small/x.fa.fastq.000000834 +# small/x.fa.fastq.000000835 +# small/x.fa.fastq.000000836 +# small/x.fa.fastq.000000837 +# small/x.fa.fastq.000000838 +# small/x.fa.fastq.000000839 +# small/x.fa.fastq.000000840 +# small/x.fa.fastq.000000841 +# small/x.fa.fastq.000000842 +# small/x.fa.fastq.000000843 +# small/x.fa.fastq.000000844 +# small/x.fa.fastq.000000845 +# small/x.fa.fastq.000000846 +# small/x.fa.fastq.000000847 +# small/x.fa.fastq.000000848 +# small/x.fa.fastq.000000849 +# small/x.fa.fastq.000000850 +# small/x.fa.fastq.000000851 +# small/x.fa.fastq.000000852 +# small/x.fa.fastq.000000853 +# small/x.fa.fastq.000000854 +# small/x.fa.fastq.000000855 +# small/x.fa.fastq.000000856 +# small/x.fa.fastq.000000857 +# small/x.fa.fastq.000000858 +# small/x.fa.fastq.000000859 +# small/x.fa.fastq.000000860 +# small/x.fa.fastq.000000861 +# small/x.fa.fastq.000000862 +# small/x.fa.fastq.000000863 +# small/x.fa.fastq.000000864 +# small/x.fa.fastq.000000865 +# small/x.fa.fastq.000000866 +# small/x.fa.fastq.000000867 +# small/x.fa.fastq.000000868 +# small/x.fa.fastq.000000869 +# small/x.fa.fastq.000000870 +# small/x.fa.fastq.000000871 +# small/x.fa.fastq.000000872 +# small/x.fa.fastq.000000873 +# small/x.fa.fastq.000000874 +# small/x.fa.fastq.000000875 +# small/x.fa.fastq.000000876 +# small/x.fa.fastq.000000877 +# small/x.fa.fastq.000000878 +# small/x.fa.fastq.000000879 +# small/x.fa.fastq.000000880 +# small/x.fa.fastq.000000881 +# small/x.fa.fastq.000000882 +# small/x.fa.fastq.000000883 +# small/x.fa.fastq.000000884 +# small/x.fa.fastq.000000885 +# small/x.fa.fastq.000000886 +# small/x.fa.fastq.000000887 +# small/x.fa.fastq.000000888 +# small/x.fa.fastq.000000889 +# small/x.fa.fastq.000000890 +# small/x.fa.fastq.000000891 +# small/x.fa.fastq.000000892 +# small/x.fa.fastq.000000893 +# small/x.fa.fastq.000000894 +# small/x.fa.fastq.000000895 +# small/x.fa.fastq.000000896 +# small/x.fa.fastq.000000897 +# small/x.fa.fastq.000000898 +# small/x.fa.fastq.000000899 +# small/x.fa.fastq.000000900 +# small/x.fa.fastq.000000901 +# small/x.fa.fastq.000000902 +# small/x.fa.fastq.000000903 +# small/x.fa.fastq.000000904 +# small/x.fa.fastq.000000905 +# small/x.fa.fastq.000000906 +# small/x.fa.fastq.000000907 +# small/x.fa.fastq.000000908 +# small/x.fa.fastq.000000909 +# small/x.fa.fastq.000000910 +# small/x.fa.fastq.000000911 +# small/x.fa.fastq.000000912 +# small/x.fa.fastq.000000913 +# small/x.fa.fastq.000000914 +# small/x.fa.fastq.000000915 +# small/x.fa.fastq.000000916 +# small/x.fa.fastq.000000917 +# small/x.fa.fastq.000000918 +# small/x.fa.fastq.000000919 +# small/x.fa.fastq.000000920 +# small/x.fa.fastq.000000921 +# small/x.fa.fastq.000000922 +# small/x.fa.fastq.000000923 +# small/x.fa.fastq.000000924 +# small/x.fa.fastq.000000925 +# small/x.fa.fastq.000000926 +# small/x.fa.fastq.000000927 +# small/x.fa.fastq.000000928 +# small/x.fa.fastq.000000929 +# small/x.fa.fastq.000000930 +# small/x.fa.fastq.000000931 +# small/x.fa.fastq.000000932 +# small/x.fa.fastq.000000933 +# small/x.fa.fastq.000000934 +# small/x.fa.fastq.000000935 +# small/x.fa.fastq.000000936 +# small/x.fa.fastq.000000937 +# small/x.fa.fastq.000000938 +# small/x.fa.fastq.000000939 +# small/x.fa.fastq.000000940 +# small/x.fa.fastq.000000941 +# small/x.fa.fastq.000000942 +# small/x.fa.fastq.000000943 +# small/x.fa.fastq.000000944 +# small/x.fa.fastq.000000945 +# small/x.fa.fastq.000000946 +# small/x.fa.fastq.000000947 +# small/x.fa.fastq.000000948 +# small/x.fa.fastq.000000949 +# small/x.fa.fastq.000000950 +# small/x.fa.fastq.000000951 +# small/x.fa.fastq.000000952 +# small/x.fa.fastq.000000953 +# small/x.fa.fastq.000000954 +# small/x.fa.fastq.000000955 +# small/x.fa.fastq.000000956 +# small/x.fa.fastq.000000957 +# small/x.fa.fastq.000000958 +# small/x.fa.fastq.000000959 +# small/x.fa.fastq.000000960 +# small/x.fa.fastq.000000961 +# small/x.fa.fastq.000000962 +# small/x.fa.fastq.000000963 +# small/x.fa.fastq.000000964 +# small/x.fa.fastq.000000965 +# small/x.fa.fastq.000000966 +# small/x.fa.fastq.000000967 +# small/x.fa.fastq.000000968 +# small/x.fa.fastq.000000969 +# small/x.fa.fastq.000000970 +# small/x.fa.fastq.000000971 +# small/x.fa.fastq.000000972 +# small/x.fa.fastq.000000973 +# small/x.fa.fastq.000000974 +# small/x.fa.fastq.000000975 +# small/x.fa.fastq.000000976 +# small/x.fa.fastq.000000977 +# small/x.fa.fastq.000000978 +# small/x.fa.fastq.000000979 +# small/x.fa.fastq.000000980 +# small/x.fa.fastq.000000981 +# small/x.fa.fastq.000000982 +# small/x.fa.fastq.000000983 +# small/x.fa.fastq.000000984 +# small/x.fa.fastq.000000985 +# small/x.fa.fastq.000000986 +# small/x.fa.fastq.000000987 +# small/x.fa.fastq.000000988 +# small/x.fa.fastq.000000989 +# small/x.fa.fastq.000000990 +# small/x.fa.fastq.000000991 +# small/x.fa.fastq.000000992 +# small/x.fa.fastq.000000993 +# small/x.fa.fastq.000000994 +# small/x.fa.fastq.000000995 +# small/x.fa.fastq.000000996 +# small/x.fa.fastq.000000997 +# small/x.fa.fastq.000000998 +# small/x.fa.fastq.000000999' +# expected: '' +not ok 4 - vg inject works perfectly for the position of alignment in the simple graph +# got: '1 +# 1 +# 1 +# 3 +# 3 +# 4 +# 4 +# 4 +# 5 +# 7 +# 7 +# 8 +# 8 +# 8 +# 9 +# 11 +# 11 +# 12 +# 12 +# 12 +# 17 +# 17 +# 17 +# 17 +# 17 +# 20 +# 20 +# 20 +# 21 +# 21 +# 25 +# 25 +# 25 +# 31 +# 31 +# 32 +# 33 +# 35 +# 37 +# 40 +# 41 +# 42 +# 45 +# 45 +# 46 +# 48 +# 48 +# 48 +# 48 +# 49 +# 49 +# 50 +# 51 +# 52 +# 52 +# 53 +# 53 +# 53 +# 53 +# 55 +# 56 +# 56 +# 58 +# 58 +# 59 +# 60 +# 60 +# 62 +# 62 +# 64 +# 64 +# 65 +# 66 +# 68 +# 69 +# 69 +# 70 +# 70 +# 70 +# 70 +# 70 +# 71 +# 72 +# 74 +# 75 +# 77 +# 77 +# 77 +# 78 +# 78 +# 78 +# 81 +# 82 +# 83 +# 84 +# 85 +# 86 +# 87 +# 87 +# 87 +# 88 +# 88 +# 88 +# 89 +# 90 +# 90 +# 93 +# 93 +# 94 +# 96 +# 96 +# 97 +# 99 +# 99 +# 100 +# 101 +# 101 +# 102 +# 102 +# 102 +# 102 +# 103 +# 103 +# 104 +# 105 +# 105 +# 106 +# 106 +# 106 +# 107 +# 108 +# 113 +# 113 +# 115 +# 116 +# 116 +# 119 +# 119 +# 120 +# 120 +# 122 +# 123 +# 124 +# 125 +# 125 +# 126 +# 126 +# 127 +# 127 +# 127 +# 128 +# 128 +# 129 +# 130 +# 130 +# 131 +# 131 +# 131 +# 132 +# 134 +# 134 +# 135 +# 136 +# 136 +# 137 +# 137 +# 137 +# 139 +# 140 +# 141 +# 142 +# 142 +# 142 +# 143 +# 143 +# 144 +# 144 +# 145 +# 145 +# 146 +# 147 +# 147 +# 149 +# 150 +# 153 +# 153 +# 154 +# 154 +# 155 +# 156 +# 156 +# 156 +# 157 +# 158 +# 158 +# 158 +# 158 +# 164 +# 164 +# 164 +# 164 +# 165 +# 166 +# 167 +# 167 +# 167 +# 167 +# 168 +# 168 +# 169 +# 170 +# 171 +# 172 +# 172 +# 173 +# 174 +# 175 +# 175 +# 175 +# 177 +# 177 +# 177 +# 178 +# 178 +# 178 +# 178 +# 180 +# 182 +# 183 +# 183 +# 184 +# 184 +# 186 +# 187 +# 188 +# 189 +# 191 +# 193 +# 194 +# 195 +# 197 +# 197 +# 197 +# 197 +# 198 +# 200 +# 200 +# 201 +# 204 +# 205 +# 205 +# 206 +# 207 +# 208 +# 209 +# 210 +# 213 +# 214 +# 214 +# 215 +# 215 +# 216 +# 217 +# 218 +# 218 +# 219 +# 219 +# 219 +# 221 +# 224 +# 224 +# 224 +# 229 +# 229 +# 232 +# 232 +# 232 +# 233 +# 234 +# 234 +# 234 +# 234 +# 237 +# 237 +# 237 +# 238 +# 239 +# 240 +# 240 +# 243 +# 244 +# 245 +# 246 +# 247 +# 250 +# 251 +# 253 +# 253 +# 255 +# 258 +# 258 +# 260 +# 262 +# 265 +# 266 +# 267 +# 268 +# 268 +# 270 +# 270 +# 270 +# 272 +# 273 +# 273 +# 274 +# 274 +# 274 +# 275 +# 276 +# 276 +# 277 +# 277 +# 280 +# 282 +# 283 +# 284 +# 285 +# 285 +# 286 +# 287 +# 287 +# 288 +# 288 +# 289 +# 290 +# 290 +# 291 +# 291 +# 291 +# 291 +# 293 +# 294 +# 294 +# 297 +# 297 +# 298 +# 298 +# 298 +# 300 +# 300 +# 304 +# 306 +# 306 +# 306 +# 307 +# 308 +# 308 +# 308 +# 309 +# 309 +# 310 +# 311 +# 311 +# 312 +# 312 +# 312 +# 313 +# 313 +# 313 +# 314 +# 314 +# 314 +# 315 +# 316 +# 317 +# 319 +# 320 +# 322 +# 323 +# 323 +# 325 +# 325 +# 326 +# 327 +# 332 +# 334 +# 334 +# 334 +# 334 +# 335 +# 336 +# 336 +# 339 +# 339 +# 340 +# 343 +# 344 +# 344 +# 344 +# 345 +# 345 +# 347 +# 347 +# 350 +# 350 +# 351 +# 353 +# 357 +# 357 +# 357 +# 358 +# 358 +# 359 +# 363 +# 363 +# 364 +# 365 +# 365 +# 366 +# 366 +# 367 +# 370 +# 372 +# 373 +# 373 +# 373 +# 375 +# 375 +# 377 +# 379 +# 379 +# 380 +# 380 +# 381 +# 383 +# 385 +# 386 +# 387 +# 389 +# 390 +# 390 +# 391 +# 394 +# 396 +# 399 +# 399 +# 400 +# 400 +# 401 +# 403 +# 403 +# 404 +# 404 +# 404 +# 405 +# 406 +# 406 +# 407 +# 407 +# 408 +# 411 +# 412 +# 412 +# 414 +# 414 +# 415 +# 415 +# 417 +# 418 +# 421 +# 423 +# 425 +# 425 +# 425 +# 425 +# 425 +# 425 +# 425 +# 426 +# 426 +# 427 +# 427 +# 427 +# 428 +# 429 +# 429 +# 430 +# 430 +# 430 +# 430 +# 431 +# 432 +# 433 +# 434 +# 434 +# 435 +# 436 +# 439 +# 440 +# 441 +# 442 +# 443 +# 447 +# 447 +# 448 +# 449 +# 449 +# 450 +# 451 +# 451 +# 452 +# 453 +# 453 +# 453 +# 454 +# 455 +# 455 +# 456 +# 457 +# 458 +# 458 +# 460 +# 460 +# 460 +# 460 +# 462 +# 462 +# 464 +# 464 +# 465 +# 465 +# 466 +# 466 +# 466 +# 467 +# 468 +# 470 +# 471 +# 471 +# 471 +# 471 +# 471 +# 472 +# 473 +# 473 +# 473 +# 474 +# 477 +# 477 +# 478 +# 478 +# 478 +# 480 +# 480 +# 481 +# 482 +# 483 +# 483 +# 483 +# 484 +# 484 +# 484 +# 487 +# 488 +# 490 +# 491 +# 492 +# 493 +# 493 +# 493 +# 494 +# 494 +# 495 +# 497 +# 500 +# 500 +# 501 +# 501 +# 502 +# 503 +# 504 +# 505 +# 506 +# 506 +# 508 +# 508 +# 510 +# 511 +# 514 +# 515 +# 516 +# 516 +# 518 +# 520 +# 521 +# 522 +# 522 +# 523 +# 523 +# 525 +# 525 +# 525 +# 526 +# 527 +# 527 +# 528 +# 530 +# 530 +# 531 +# 532 +# 533 +# 535 +# 537 +# 537 +# 537 +# 538 +# 539 +# 542 +# 544 +# 545 +# 546 +# 546 +# 547 +# 549 +# 549 +# 551 +# 551 +# 552 +# 552 +# 552 +# 553 +# 554 +# 554 +# 556 +# 557 +# 558 +# 558 +# 560 +# 561 +# 563 +# 565 +# 565 +# 566 +# 567 +# 567 +# 569 +# 569 +# 569 +# 570 +# 571 +# 572 +# 572 +# 572 +# 572 +# 573 +# 575 +# 577 +# 578 +# 579 +# 581 +# 582 +# 584 +# 584 +# 585 +# 585 +# 588 +# 589 +# 590 +# 593 +# 593 +# 595 +# 596 +# 597 +# 598 +# 599 +# 600 +# 600 +# 600 +# 600 +# 601 +# 601 +# 602 +# 602 +# 603 +# 604 +# 605 +# 605 +# 606 +# 608 +# 608 +# 608 +# 609 +# 611 +# 612 +# 612 +# 613 +# 613 +# 614 +# 614 +# 615 +# 615 +# 615 +# 616 +# 618 +# 618 +# 619 +# 619 +# 620 +# 620 +# 620 +# 622 +# 625 +# 625 +# 626 +# 626 +# 627 +# 628 +# 629 +# 629 +# 630 +# 630 +# 630 +# 631 +# 632 +# 632 +# 634 +# 634 +# 634 +# 636 +# 636 +# 636 +# 637 +# 637 +# 639 +# 639 +# 639 +# 641 +# 642 +# 642 +# 644 +# 644 +# 645 +# 649 +# 650 +# 650 +# 651 +# 654 +# 655 +# 656 +# 656 +# 657 +# 658 +# 660 +# 661 +# 661 +# 663 +# 667 +# 668 +# 668 +# 671 +# 672 +# 674 +# 674 +# 674 +# 675 +# 676 +# 676 +# 676 +# 676 +# 677 +# 677 +# 680 +# 681 +# 683 +# 684 +# 684 +# 687 +# 688 +# 690 +# 692 +# 693 +# 693 +# 693 +# 696 +# 697 +# 697 +# 700 +# 700 +# 701 +# 702 +# 702 +# 702 +# 703 +# 703 +# 704 +# 704 +# 704 +# 704 +# 705 +# 706 +# 706 +# 707 +# 707 +# 711 +# 713 +# 713 +# 714 +# 718 +# 720 +# 722 +# 723 +# 724 +# 724 +# 724 +# 725 +# 726 +# 726 +# 726 +# 728 +# 729 +# 729 +# 730 +# 733 +# 734 +# 734 +# 735 +# 738 +# 738 +# 738 +# 741 +# 743 +# 746 +# 747 +# 749 +# 751 +# 752 +# 752 +# 753 +# 754 +# 755 +# 756 +# 758 +# 758 +# 759 +# 759 +# 760 +# 761 +# 761 +# 762 +# 763 +# 763 +# 764 +# 765 +# 767 +# 767 +# 768 +# 769 +# 770 +# 770 +# 770 +# 771 +# 771 +# 771 +# 775 +# 776 +# 776 +# 777 +# 779 +# 779 +# 779 +# 779 +# 781 +# 781 +# 782 +# 785 +# 787 +# 787 +# 787 +# 788 +# 789 +# 789 +# 790 +# 790 +# 791 +# 791 +# 792 +# 792 +# 792 +# 793 +# 793 +# 793 +# 794 +# 796 +# 796 +# 802 +# 806 +# 806 +# 807 +# 808 +# 809 +# 809 +# 809 +# 810 +# 810 +# 812 +# 813 +# 818 +# 825 +# 825 +# 826 +# 826 +# 827 +# 827 +# 828 +# 829 +# 830 +# 830 +# 834 +# 834 +# 835 +# 835 +# 836 +# 837 +# 841 +# 844 +# 845 +# 845 +# 845 +# 845 +# 846 +# 846 +# 850 +# 850 +# 852 +# 853 +# 853 +# 854 +# 855 +# 856 +# 858 +# 859 +# 860 +# 861 +# 862 +# 862 +# 863 +# 864 +# 866 +# 869 +# 870 +# 870 +# 871 +# 873 +# 874 +# 874 +# 876 +# 877 +# 877 +# 877 +# 877 +# 879 +# 881 +# 882 +# 883 +# 884 +# 885 +# 885 +# 885 +# 886 +# 887 +# 888 +# 889 +# 889 +# 889 +# 889 +# 889 +# 890 +# 890 +# 890 +# 890 +# 891 +# 892 +# 892 +# 892 +# 895 +# 895 +# 895 +# 896 +# 896 +# 896 +# 896 +# 896 +# 897 +# 898 +# 898 +# 898 +# 899 +# 900 +# 900 +# 901' +# expected: '' +not ok 5 - vg inject works perfectly for the position of alignment +# got: '1 +# 1 +# 1 +# 3 +# 3 +# 4 +# 4 +# 4 +# 5 +# 7 +# 7 +# 8 +# 8 +# 8 +# 9 +# 11 +# 11 +# 12 +# 12 +# 12 +# 17 +# 17 +# 17 +# 17 +# 17 +# 20 +# 20 +# 20 +# 21 +# 21 +# 25 +# 25 +# 25 +# 31 +# 31 +# 32 +# 33 +# 35 +# 37 +# 40 +# 41 +# 42 +# 45 +# 45 +# 46 +# 48 +# 48 +# 48 +# 48 +# 49 +# 49 +# 50 +# 51 +# 52 +# 52 +# 53 +# 53 +# 53 +# 53 +# 55 +# 56 +# 56 +# 58 +# 58 +# 59 +# 60 +# 60 +# 62 +# 62 +# 64 +# 64 +# 65 +# 66 +# 68 +# 69 +# 69 +# 70 +# 70 +# 70 +# 70 +# 70 +# 71 +# 72 +# 74 +# 75 +# 77 +# 77 +# 77 +# 78 +# 78 +# 78 +# 81 +# 82 +# 83 +# 84 +# 85 +# 86 +# 87 +# 87 +# 87 +# 88 +# 88 +# 88 +# 89 +# 90 +# 90 +# 93 +# 93 +# 94 +# 96 +# 96 +# 97 +# 99 +# 99 +# 100 +# 101 +# 101 +# 102 +# 102 +# 102 +# 102 +# 103 +# 103 +# 104 +# 105 +# 105 +# 106 +# 106 +# 106 +# 107 +# 108 +# 113 +# 113 +# 115 +# 116 +# 116 +# 119 +# 119 +# 120 +# 120 +# 122 +# 123 +# 124 +# 125 +# 125 +# 126 +# 126 +# 127 +# 127 +# 127 +# 128 +# 128 +# 129 +# 130 +# 130 +# 131 +# 131 +# 131 +# 132 +# 134 +# 134 +# 135 +# 136 +# 136 +# 137 +# 137 +# 137 +# 139 +# 140 +# 141 +# 142 +# 142 +# 142 +# 143 +# 143 +# 144 +# 144 +# 145 +# 145 +# 146 +# 147 +# 147 +# 149 +# 150 +# 153 +# 153 +# 154 +# 154 +# 155 +# 156 +# 156 +# 156 +# 157 +# 158 +# 158 +# 158 +# 158 +# 164 +# 164 +# 164 +# 164 +# 165 +# 166 +# 167 +# 167 +# 167 +# 167 +# 168 +# 168 +# 169 +# 170 +# 171 +# 172 +# 172 +# 173 +# 174 +# 175 +# 175 +# 175 +# 177 +# 177 +# 177 +# 178 +# 178 +# 178 +# 178 +# 180 +# 182 +# 183 +# 183 +# 184 +# 184 +# 186 +# 187 +# 188 +# 189 +# 191 +# 193 +# 194 +# 195 +# 197 +# 197 +# 197 +# 197 +# 198 +# 200 +# 200 +# 201 +# 204 +# 205 +# 205 +# 206 +# 207 +# 208 +# 209 +# 210 +# 213 +# 214 +# 214 +# 215 +# 215 +# 216 +# 217 +# 218 +# 218 +# 219 +# 219 +# 219 +# 221 +# 224 +# 224 +# 224 +# 229 +# 229 +# 232 +# 232 +# 232 +# 233 +# 234 +# 234 +# 234 +# 234 +# 237 +# 237 +# 237 +# 238 +# 239 +# 240 +# 240 +# 243 +# 244 +# 245 +# 246 +# 247 +# 250 +# 251 +# 253 +# 253 +# 255 +# 258 +# 258 +# 260 +# 262 +# 265 +# 266 +# 267 +# 268 +# 268 +# 270 +# 270 +# 270 +# 272 +# 273 +# 273 +# 274 +# 274 +# 274 +# 275 +# 276 +# 276 +# 277 +# 277 +# 280 +# 282 +# 283 +# 284 +# 285 +# 285 +# 286 +# 287 +# 287 +# 288 +# 288 +# 289 +# 290 +# 290 +# 291 +# 291 +# 291 +# 291 +# 293 +# 294 +# 294 +# 297 +# 297 +# 298 +# 298 +# 298 +# 300 +# 300 +# 304 +# 306 +# 306 +# 306 +# 307 +# 308 +# 308 +# 308 +# 309 +# 309 +# 310 +# 311 +# 311 +# 312 +# 312 +# 312 +# 313 +# 313 +# 313 +# 314 +# 314 +# 314 +# 315 +# 316 +# 317 +# 319 +# 320 +# 322 +# 323 +# 323 +# 325 +# 325 +# 326 +# 327 +# 332 +# 334 +# 334 +# 334 +# 334 +# 335 +# 336 +# 336 +# 339 +# 339 +# 340 +# 343 +# 344 +# 344 +# 344 +# 345 +# 345 +# 347 +# 347 +# 350 +# 350 +# 351 +# 353 +# 357 +# 357 +# 357 +# 358 +# 358 +# 359 +# 363 +# 363 +# 364 +# 365 +# 365 +# 366 +# 366 +# 367 +# 370 +# 372 +# 373 +# 373 +# 373 +# 375 +# 375 +# 377 +# 379 +# 379 +# 380 +# 380 +# 381 +# 383 +# 385 +# 386 +# 387 +# 389 +# 390 +# 390 +# 391 +# 394 +# 396 +# 399 +# 399 +# 400 +# 400 +# 401 +# 403 +# 403 +# 404 +# 404 +# 404 +# 405 +# 406 +# 406 +# 407 +# 407 +# 408 +# 411 +# 412 +# 412 +# 414 +# 414 +# 415 +# 415 +# 417 +# 418 +# 421 +# 423 +# 425 +# 425 +# 425 +# 425 +# 425 +# 425 +# 425 +# 426 +# 426 +# 427 +# 427 +# 427 +# 428 +# 429 +# 429 +# 430 +# 430 +# 430 +# 430 +# 431 +# 432 +# 433 +# 434 +# 434 +# 435 +# 436 +# 439 +# 440 +# 441 +# 442 +# 443 +# 447 +# 447 +# 448 +# 449 +# 449 +# 450 +# 451 +# 451 +# 452 +# 453 +# 453 +# 453 +# 454 +# 455 +# 455 +# 456 +# 457 +# 458 +# 458 +# 460 +# 460 +# 460 +# 460 +# 462 +# 462 +# 464 +# 464 +# 465 +# 465 +# 466 +# 466 +# 466 +# 467 +# 468 +# 470 +# 471 +# 471 +# 471 +# 471 +# 471 +# 472 +# 473 +# 473 +# 473 +# 474 +# 477 +# 477 +# 478 +# 478 +# 478 +# 480 +# 480 +# 481 +# 482 +# 483 +# 483 +# 483 +# 484 +# 484 +# 484 +# 487 +# 488 +# 490 +# 491 +# 492 +# 493 +# 493 +# 493 +# 494 +# 494 +# 495 +# 497 +# 500 +# 500 +# 501 +# 501 +# 502 +# 503 +# 504 +# 505 +# 506 +# 506 +# 508 +# 508 +# 510 +# 511 +# 514 +# 515 +# 516 +# 516 +# 518 +# 520 +# 521 +# 522 +# 522 +# 523 +# 523 +# 525 +# 525 +# 525 +# 526 +# 527 +# 527 +# 528 +# 530 +# 530 +# 531 +# 532 +# 533 +# 535 +# 537 +# 537 +# 537 +# 538 +# 539 +# 542 +# 544 +# 545 +# 546 +# 546 +# 547 +# 549 +# 549 +# 551 +# 551 +# 552 +# 552 +# 552 +# 553 +# 554 +# 554 +# 556 +# 557 +# 558 +# 558 +# 560 +# 561 +# 563 +# 565 +# 565 +# 566 +# 567 +# 567 +# 569 +# 569 +# 569 +# 570 +# 571 +# 572 +# 572 +# 572 +# 572 +# 573 +# 575 +# 577 +# 578 +# 579 +# 581 +# 582 +# 584 +# 584 +# 585 +# 585 +# 588 +# 589 +# 590 +# 593 +# 593 +# 595 +# 596 +# 597 +# 598 +# 599 +# 600 +# 600 +# 600 +# 600 +# 601 +# 601 +# 602 +# 602 +# 603 +# 604 +# 605 +# 605 +# 606 +# 608 +# 608 +# 608 +# 609 +# 611 +# 612 +# 612 +# 613 +# 613 +# 614 +# 614 +# 615 +# 615 +# 615 +# 616 +# 618 +# 618 +# 619 +# 619 +# 620 +# 620 +# 620 +# 622 +# 625 +# 625 +# 626 +# 626 +# 627 +# 628 +# 629 +# 629 +# 630 +# 630 +# 630 +# 631 +# 632 +# 632 +# 634 +# 634 +# 634 +# 636 +# 636 +# 636 +# 637 +# 637 +# 639 +# 639 +# 639 +# 641 +# 642 +# 642 +# 644 +# 644 +# 645 +# 649 +# 650 +# 650 +# 651 +# 654 +# 655 +# 656 +# 656 +# 657 +# 658 +# 660 +# 661 +# 661 +# 663 +# 667 +# 668 +# 668 +# 671 +# 672 +# 674 +# 674 +# 674 +# 675 +# 676 +# 676 +# 676 +# 676 +# 677 +# 677 +# 680 +# 681 +# 683 +# 684 +# 684 +# 687 +# 688 +# 690 +# 692 +# 693 +# 693 +# 693 +# 696 +# 697 +# 697 +# 700 +# 700 +# 701 +# 702 +# 702 +# 702 +# 703 +# 703 +# 704 +# 704 +# 704 +# 704 +# 705 +# 706 +# 706 +# 707 +# 707 +# 711 +# 713 +# 713 +# 714 +# 718 +# 720 +# 722 +# 723 +# 724 +# 724 +# 724 +# 725 +# 726 +# 726 +# 726 +# 728 +# 729 +# 729 +# 730 +# 733 +# 734 +# 734 +# 735 +# 738 +# 738 +# 738 +# 741 +# 743 +# 746 +# 747 +# 749 +# 751 +# 752 +# 752 +# 753 +# 754 +# 755 +# 756 +# 758 +# 758 +# 759 +# 759 +# 760 +# 761 +# 761 +# 762 +# 763 +# 763 +# 764 +# 765 +# 767 +# 767 +# 768 +# 769 +# 770 +# 770 +# 770 +# 771 +# 771 +# 771 +# 775 +# 776 +# 776 +# 777 +# 779 +# 779 +# 779 +# 779 +# 781 +# 781 +# 782 +# 785 +# 787 +# 787 +# 787 +# 788 +# 789 +# 789 +# 790 +# 790 +# 791 +# 791 +# 792 +# 792 +# 792 +# 793 +# 793 +# 793 +# 794 +# 796 +# 796 +# 802 +# 806 +# 806 +# 807 +# 808 +# 809 +# 809 +# 809 +# 810 +# 810 +# 812 +# 813 +# 818 +# 825 +# 825 +# 826 +# 826 +# 827 +# 827 +# 828 +# 829 +# 830 +# 830 +# 834 +# 834 +# 835 +# 835 +# 836 +# 837 +# 841 +# 844 +# 845 +# 845 +# 845 +# 845 +# 846 +# 846 +# 850 +# 850 +# 852 +# 853 +# 853 +# 854 +# 855 +# 856 +# 858 +# 859 +# 860 +# 861 +# 862 +# 862 +# 863 +# 864 +# 866 +# 869 +# 870 +# 870 +# 871 +# 873 +# 874 +# 874 +# 876 +# 877 +# 877 +# 877 +# 877 +# 879 +# 881 +# 882 +# 883 +# 884 +# 885 +# 885 +# 885 +# 886 +# 887 +# 888 +# 889 +# 889 +# 889 +# 889 +# 889 +# 890 +# 890 +# 890 +# 890 +# 891 +# 892 +# 892 +# 892 +# 895 +# 895 +# 895 +# 896 +# 896 +# 896 +# 896 +# 896 +# 897 +# 898 +# 898 +# 898 +# 899 +# 900 +# 900 +# 901' +# expected: '' +not ok 6 - vg inject works perfectly for the mapping quality of alignment +# got: '1000' # expected: '0' -ok 8 - node size is manageable by default -ok 9 - construction of a very complex region succeeds -ok 10 - the complex graph has the expected number of nodes -ok 11 - the complex graph has the expected number of edges -ok 12 - the ordering of variants at the same position has no effect on the resulting graph -ok 13 - construction does not fail when the first position in the VCF is repeated and has an indel -ok 14 - the size of the regions used in construction has no effect on the graph -ok 15 - the number of threads used in construction has no effect on the graph -ok 16 - the number of threads and regions used in construction has no effect on the graph -ok 17 - construction of a graph with two head nodes succeeds -ok 18 - the graph contains all the sequence in the reference and VCF -ok 19 - varying the max node size does not affect graph length -ok 20 - nodes are correctly capped in size -ok 21 - -R --region flag is respected -ok 22 - vg construct does not require a vcf -ok 23 - vg construct respects node size limit -ok 24 - --region can be interpreted to be a reference sequence (and not parsed as a region spec) -ok 25 - vg constructs the correct graph for inversions -ok 26 - vg construct skips variants with . ALTs -ok 27 - VCF with * alleles is accepted -ok 28 - VCF record with * allele is rejected -ok 29 - Reference with ambiguity codes has them coerced to Ns -ok 30 - Expected number of Ns are created -Failed 1/30 subtests -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -error[VPKG::load_one]: Could not open test/graphs/rgfa_with_reference.rgfa while loading handlegraph::PathHandleGraph -error:[get_input_file_name] unable to open input file: test/graphs/rgfa_with_reference.rgfa -error[VPKG::load_one]: Could not open test/graphs/rgfa_with_reference.rgfa while loading handlegraph::PathHandleGraph -error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph -error[VPKG::load_one]: Could not open test/graphs/gfa_with_reference.gfa while loading handlegraph::PathHandleGraph -error:[get_input_file_name] unable to open input file: test/graphs/gfa_with_reference.gfa -error[VPKG::load_one]: Could not open test/graphs/gfa_with_reference.gfa while loading handlegraph::PathHandleGraph -error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph -t/03_vg_view.t ........ -1..23 -ok 1 - view produces the expected number of lines of dot output -ok 2 - view produces the expected number of lines of GFA output -ok 3 - view converts back and forth between GFA and vg format -ok 4 - view can convert BAM to GAM -ok 5 - view can round-trip JSON and GAM -ok 6 - view can round-trip qualities and encodes tham as PHRED+0 base-64-encoded strings in JSON -ok 7 - view can reconstruct a VG graph from JSON -ok 8 - view can pass through VG when loading as vg::VG -ok 9 - view can pass through semantically identical VG normally -ok 10 - view parses sample names -ok 11 - view can handle fastq input -ok 12 - view can translate graphs with 2-node cycles -ok 13 - view outputs properly oriented GFA -ok 14 - view produces the expected number of lines of dot output from a cyclic graph -ok 15 - streaming JSON output produces the expected number of chunks -ok 16 - duplicate warnings can be suppressed when loading as vg::VG -ok 17 - gfa graphs with overlaps are rejected -ok 18 - GFA import produces a concise error message when overlaps are present -ok 19 - GFA import rejects a GFA file with an overlap that goes beyond its sequences -ok 20 - GFA import produces a concise error message in that case -ok 21 - vg view preserves path metadata of rGFA file -ok 22 - vg view preserves path metadata of GFA file -ok 23 - vg view can emit a GFA file with subranges on a haplotype without explicit phase blocks -ok -[vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes -t/04_vg_align.t ....... -1..20 -ok 1 - alignment traverses the correct path -ok 2 - alignment score is as expected -ok 3 - full length bonus works and is included by default -ok 4 - bonuses are included on only one end for pinned alignments -ok 5 - scoring parameters are respected -ok 6 - score-matrix file should give same results as --match 2 --mismatch 2: scoring parameters are respected -ok 7 - alignment does not contain excessive soft clips under lenient scoring -ok 8 - score-matrix file should give same results as --match 2 --mismatch 2: alignment does not contain excessive soft clips under lenient scoring -ok 9 - alignment score does not overflow at 255 when using 8x16bit vectors -ok 10 - score-matrix file should give same results as --match 2 --mismatch 2: alignment score does not overflow at 255 when using 8x16bit vectors -ok 11 - Ns do not cause excessive soft clipping -ok 12 - nodes are only referenced if they have mappings -ok 13 - align can use query names and outputs GAM -ok 14 - alignment to cyclic graphs works -ok 15 - graphs where duplicated nodes need flipping can be used for alignment -ok 16 - node flipping doesn't destroy the alignment -ok 17 - alignment correctly handles an inversion -ok 18 - the exploding graph doesn't blow up -ok 19 - pinning doesn't cause problems for gssw -ok 20 - left pinning is correctly handled -ok -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -t/05_vg_find.t ........ -1..29 -ok 1 - construction -ok 2 - a path can be queried from the xg index -ok 3 - a node near another can be obtained using context from the xg index -ok 4 - each perfect read contains one maximal exact match -ok 5 - vg find -D finds approximate distance between 2 adjacent node starts -ok 6 - vg find -D finds approximate distance between node start and adjacent snp -ok 7 - vg find -D jumps deletion -ok 8 - vg find -D jumps deletion from other allele in snp -ok 9 - vg find -L finds same number of nodes (with -c 1) -ok 10 - vg find -L works with -r. it scans from start position of first node in range -ok 11 - vg find -L tracks length from start position of input node -ok 12 - vg find -L works with more than one input node -ok 13 - we find the 4 canonical SMEMs from @lh3's bwa mem poster -ok 14 - we can find the right MEMs for a sequence with Ns -ok 15 - we find the same MEMs sequences with different lengths of Ns -ok 16 - the GAM index can return the set of alignments mapping to a node -ok 17 - a subgraph query may be used to obtain a particular subset of alignments from a sorted GAM -ok 18 - the index can be queried using GAM alignments -ok 19 - find gets connected edges between queried nodes by default -ok 20 - find gets nodes provided in a node file list -ok 21 - extracting by path adds no extra edges -ok 22 - pattern based path extraction works -ok 23 - path DAG range query works -ok 24 - we can extract a set of targets to separate files -ok 25 - the same extraction can be made using BED input -ok 26 - we see the expected number of kmers in the given targets -ok 27 - we find the expected number of kmers with haplotype frequency equal to 2 -ok 28 - GFA i/o for find -n consistent with converting both ways -ok 29 - find nodes that map to the provided node ids -ok - -WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -warning: -i option is deprecated - -WARNING:[vg] Subcommand 'concat' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -[vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. -t/06_vg_index.t ....... -1..54 -ok 1 - building an XG index of a graph -ok 2 - building a GCSA index of a graph -ok 3 - building both indexes at once -ok 4 - the indexes are identical when built one at a time and together -ok 5 - building GCSA from XG -ok 6 - the GCSA indexes are identical when built from vg and from xg -ok 7 - building a GBWT index of a graph with haplotypes -ok 8 - building an XG index of a graph with haplotypes -ok 9 - xg index does not contain alt paths by default -ok 10 - building an XG index of a graph with haplotypes and alt paths included -ok 11 - xg index does contains alt paths with index -L -ok 12 - building a GCSA index of a graph with haplotypes -ok 13 - building all indexes at once -ok 14 - the indexes are identical -ok 15 - building all indexes at once, while leaving alt paths in xg -ok 16 - the indexes are identical with -L -ok 17 - xg index does contains alt paths with index -L all at once -ok 18 - samples can be excluded from haplotype indexing -ok 19 - excluded samples were not included in the GBWT index -ok 20 - GBWT from GAF same as from GAM -ok 21 - building GBWT index for a regional graph -ok 22 - no warnings about missing variants produced -ok 23 - building an XG index of multiple graphs -ok 24 - building a GCSA index of multiple graphs -ok 25 - building both indexes at once -ok 26 - the indexes are identical -ok 27 - building a GBWT index of multiple graphs with haplotypes -ok 28 - building an XG index of multiple graphs with haplotypes -ok 29 - building a GCSA index of multiple graphs with haplotypes -ok 30 - building XG and GCSA indexes at once -ok 31 - building an XG index with alt paths -ok 32 - building a GBWT index from an XG index -ok 33 - the indexes are identical -ok 34 - GBWT can be built for paths -ok 35 - fail with nonexistent file -ok 36 - a prebuilt deBruijn graph in GCSA2 format may be used -ok 37 - vg index and vg gamsort produce identical sorted GAM indexes -ok 38 - storage of multiple graphs in an index succeeds -ok 39 - can index backward nodes -ok 40 - can index kmers for backward nodes -ok 41 - GCSA2 index works on cyclic graphs with heads and tails -ok 42 - GCSA2 index works on cyclic graphs with no heads or tails -ok 43 - GCSA2 index works on cyclic graphs with self loops -ok 44 - GCSA2 index works on general cyclic graphs -ok 45 - GCSA2 indexing of a tiny graph works -ok 46 - GCSA2 indexing succeeds on a single-node graph -ok 47 - GCSA2 indexing succeeds on graph with heads but no tails -ok 48 - a useful error message is produced when nodes are too large -ok 49 - snarl finding with trivial snarls -ok 50 - building a distance index of a graph -ok 51 - building a distance index of a piped vg graph -ok 52 - building a distance index of a piped PackedGraph -ok 53 - distance index construction from GBZ -ok 54 - distance index construction from piped GBZ -ok -warning: Thread 0 encountered sequence of length 100, which is longer than the non-chunked limit of 30. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -[vg::alignment.cpp] couldn't open reads/NONEXISTENT -[vg::alignment.cpp] couldn't open reads/NONEXISTENT -[vg::alignment.cpp] couldn't open reads/NONEXISTENT -[vg::alignment.cpp] couldn't open reads/NONEXISTENT -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -index file t.fa.fai not found, generating... -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -t/07_vg_map.t ......... -1..55 -ok 1 - offset counts unused bases from the start of the node on the forward strand -ok 2 - xdrop alignment obtains the expected result -ok 3 - xdrop alignment obtains the expected result for the reverse complement -ok 4 - score-matrix defaults match 1 mismatch -4 should produce same results: with matrixoffset counts unused bases from the start of the node on the forward strand -ok 5 - offset counts unused bases from the start of the node on the reverse strand -ok 6 - global alignment traverses the correct path -ok 7 - alignment score is as expected -ok 8 - scoring parameters are respected -ok 9 - score-matrix file should give same results as --match 2 --mismatch 2: scoring parameters are respected -ok 10 - full length bonus always be included -ok 11 - full length bonus can be set to 0 -ok 12 - vg map takes -d as input without a variant graph -ok 13 - vg map can align across a SNP -ok 14 - alignment works on a small graph -ok 15 - binary alignment format is equivalent to json version -ok 16 - alignment from BAM correctly handles qualities -ok 17 - chunky-banded alignment works -ok 18 - multiple alignments are returned in descending score order -ok 19 - only a single primary alignment is returned -ok 20 - vg can map multi-line FASTA sequences -ok 21 - mapping of BAM file produces expected number of alignments -ok 22 - mapping from a fastq produces the expected number of alignments -ok 23 - allowing secondary alignments with MEM mapping does not change number of primary alignments -ok 24 - vg connects paired-end reads in gam output -ok 25 - mapping to graphs that can't be oriented without swapping edges works correctly -ok 26 - reads multi-map to multiple possible locations -ok 27 - vg map works based on gcsa and xg indexes -ok 28 - the mapping quality may be capped -ok 29 - paired read alignments forced to be consistent have lower score than unrestricted alignments -ok 30 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments -ok 31 - only primary alignments have mapping quality scores -ok 32 - unpaired reads produce mapping quality scores -ok 33 - map returns same output on xg and vg (single threaded) -ok 34 - base quality adjusted alignment produces higher scores if mismatches have low quality -ok 35 - error on vg map -f (unpaired) -ok 36 - error on vg map -f (interleaved) -ok 37 - error on vg map -f (paired, LHS) -ok 38 - error on vg map -f (paired, RHS) -ok 39 - mapping a read that touches unused nodes gets the base score -ok 40 - mapping a read that matches a haplotype gets a small penalty -ok 41 - mapping a read that matches a haplotype with exponent 0 gets the base score -ok 42 - mapping a read that matches no haplotypes gets a larger penalty -ok 43 - surjection of paired reads to SAM yields correct positions -ok 44 - surjection of paired reads to SAM yields correct pair partner positions -ok 45 - surjection of paired reads to SAM yields properly matched QNAMEs -ok 46 - surjection of paired reads to SAM produces correct pair partner contigs -ok 47 - surjection of paired reads to SAM produces correct flags -ok 48 - surjection of unpaired reads to SAM yields correct positions -ok 49 - surjection of unpaired reads to SAM yields correct pair partner positions -ok 50 - surjection of unpaired reads to SAM yields distinct QNAMEs -ok 51 - surjection of unpaired reads to SAM produces absent partner contigs -ok 52 - surjection of unpaired reads to SAM produces correct flags -ok 53 - mapper can read FASTA input -ok 54 - mapper can read multiline FASTA input -ok 55 - xdrop works on a reversed read -ok -[vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. -t/08_vg_ids.t ......... -1..10 -ok 1 - minimum node as expected (id compaction correct) -ok 2 - maximum node is as expected (id compaction correct) -ok 3 - correctly generated joint id space for several graphs -ok 4 - can sort and re-number a graph with self loops -ok 5 - can sort and renumber a complex cyclic graph -ok 6 - sorting removes back-edges in a DAG -ok 7 - sorting assigns node IDs in topological order -ok 8 - sorting does not affect id range -ok 9 - sorting does not affect id range of vg -ok 10 - sorting does not affect id range of hg -ok - -WARNING:[vg] Subcommand 'concat' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - - -WARNING:[vg] Subcommand 'concat' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. - -WARNING:[vg] Subcommand 'concat' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - - -WARNING:[vg] Subcommand 'concat' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -t/09_vg_concat.t ...... -1..4 -ok 1 - concat doubles the number of nodes -ok 2 - concat doubles the number of edges + 1 -ok 3 - concat -p doubles the number of nodes on reversing graph -ok 4 - concat -p doubles the number of edges + 1 on reversing graph -ok -t/100_code_quality.t .. -1..1 -ok 1 - code quality is acceptable -ok -warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;END=1017354;NS=2504;SVLEN=-3562;SVTYPE=DEL;DP=15541;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0 ! -warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AN=5008;CS=ALU_umary;MEINFO=AluUndef,2,281,+;NS=2504;SVLEN=279;SVTYPE=ALU;TSD=null;DP=18053;EAS_AF=0;AMR_AF=0.0043;AFR_AF=0.0303;EUR_AF=0;SAS_AF=0 ! -warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 490168 DUP_gs_CNV_20_1490168_1549769 G 100 PASS AC=1;AF=0.000199681;AN=5008;CS=DUP_gs;END=1549769;NS=2504;SVTYPE=DUP;DP=21874;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0.001 ! -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -[vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. -[vg autoindex] Executing command: vg autoindex -v tiny/tiny.vcf.gz -r tiny/tiny.fa -w giraffe -p tiny -[IndexRegistry]: Checking for phasing in VCF(s). -[IndexRegistry]: Chunking inputs for parallelism. -[IndexRegistry]: Constructing VG graph from FASTA and VCF input. -[IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. -[IndexRegistry]: Stripping allele paths from VG. -[IndexRegistry]: Constructing XG graph from VG graph. -[IndexRegistry]: Downsampling full GBWT. -[IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. -[IndexRegistry]: Constructing GBZ. -[IndexRegistry]: Constructing distance index for Giraffe. -[IndexRegistry]: Constructing minimizer index. -warning:[GFAParser] Ignoring unrecognized # line type -t/10_vg_stats.t ....... -1..21 -ok 1 - vg stats reports the expected number of nodes -ok 2 - vg stats reports the expected number of edges -ok 3 - vg stats reports the expected graph length -ok 4 - vg stats reports the correct number of subgraphs -ok 5 - vg stats reports the correct subgraph length -ok 6 - distance to head is correct -ok 7 - distance to tail is correct -ok 8 - aligned read stats are computed correctly -ok 9 - basic stats agree between graph formats -ok 10 - stats can be computed for GAM files without graphs -ok 11 - a path overlap description of a test graph has the expected length -ok 12 - vg stats -F detects format of old protobuf graph -ok 13 - vg stats -F detects format of newer protobuf graph -ok 14 - vg stats -F detects format of hash graph -ok 15 - vg stats -F detects format of packed graph -ok 16 - vg stats -F detects format of xg graph -ok 17 - vg stats -F detects format of GFA graph -ok 18 - vg stats -F detects format of GBZ graph -ok 19 - vg stats -D found correct degree distribution of tiny graph -ok 20 - vg stats -L counts self-loops correctly -ok 21 - vg stats -e finds the right nondeterministic edge sets -ok - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 68, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 54, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -t/11_vg_paths.t ....... -1..20 -ok 1 - path listing works from vg -ok 2 - path listing works from XG -ok 3 - generic path listing works from XG -ok 4 - thread listing works from GBWT -ok 5 - haplotype thread listing works from GBWT -ok 6 - thread selection by name prefix works correctly -ok 7 - thread selection by sample name works correctly -ok 8 - no threads are reported for invalid samples -ok 9 - vg paths may be used to extract threads -ok 10 - vg paths may be used to extract threads as GAF -ok 11 - Fasta extracted from xg is the same as the input fasta -ok 12 - Fasta extracted from vg is the same as the input fasta -ok 13 - Fasta extracted from threads has correct number of lines -ok 14 - a single path may be retained -ok 15 - path filtering does not modify the graph -ok 16 - alt allele paths can be dropped -ok 17 - vg path coverage has correct number of columns -ok 18 - vg path coverage has correct number of rows -ok 19 - vg paths found correct number of lengths -ok 20 - vg path coverage reports correct lengths in first column -ok - -WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - - -WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - - -WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - - -WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - - -WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - - -WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - - -WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - - -WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - - -WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -warning[vg mod]: -o is deprecated. Dangling edges are now automatically removed.[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. - - -WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -t/12_vg_kmers.t ....... -1..10 -ok 1 - correct numbers of kmers in the graph -ok 2 - to_end edges are handled correctly -ok 3 - from_start edges are handled correctly -ok 4 - GCSA2 output produces the expected number of lines -ok 5 - GCSA2 binary output produces the expected number bytes -ok 6 - GCSA2 output works when next position is multiple -ok 7 - GCSA2 output works when previous characters are multiple -ok 8 - edge-max correctly bounds the number of kmers in a complex graph -ok 9 - start/stop node IDs can be specified in GCSA2 output -ok 10 - attempting to generate kmers longer than the longest path in a graph correctly yields no kmers -ok -index file n.fa.fai not found, generating... -warning: [HaplotypeIndexer::parse_vcf] contig y not present in file small/x.vcf.gz -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -t/13_vg_sim.t ......... -1..36 -ok 1 - vg sim creates the correct number of reads -ok 2 - end bonuses are included -ok 3 - alignments may be generated rather than read sequences -ok 4 - alignments are produced on both strands -ok 5 - high simulated error rates do not change the number of bases generated -ok 6 - vg sim creates forward-strand reads when asked -ok 7 - vg sim can simulate from just a path -ok 8 - vg sim can simulate from just a path in FASTQ mode -ok 9 - reads can be simulated from all paths -ok 10 - simulation was successful -ok 11 - reads can be simulated from GBWT samples -ok 12 - simulation was successful -ok 13 - pairs simulated even when fragments overlap -ok 14 - sim does not emit reads with Ns -ok 15 - sim can emit reads with Ns when asked to -ok 16 - sim doesn't emit Ns even with pair and errors -ok 17 - Sample simulation works along with --any-path -ok 18 - not having any regexes skips all unvisited contigs -ok 19 - assigning a ploidy of 2 by default gives reads in a ~1-1 ratio vs. diploid covered contigs -ok 20 - assigning a ploidy of 1 by regex gives reads in a ~1-2 ratio vs. diploid covered contigs -ok 21 - assigning a ploidy of 0 by regex excludes reads from that contig -ok 22 - multiple regexes are interpreted -ok 23 - regexes are interpreted as regexes -ok 24 - assigning a very high ploidy by regex starves out the other paths -ok 25 - Sample simulation works along with --any-path with training FASTQ -ok 26 - not having any regexes skips all unvisited contigs with training FASTQ -ok 27 - assigning a ploidy of 2 by default gives reads in a ~1-1 ratio vs. diploid covered contigs with training FASTQ -ok 28 - assigning a ploidy of 1 by regex gives reads in a ~1-2 ratio vs. diploid covered contigs with training FASTQ -ok 29 - assigning a ploidy of 0 by regex excludes reads from that contig with training FASTQ -ok 30 - multiple regexes are interpreted with training FASTQ -ok 31 - regexes are interpreted as regexes with training FASTQ -ok 32 - assigning a very high ploidy by regex starves out the other paths with training FASTQ -ok 33 - All reads are annotated with single reference positions by default -ok 34 - All reads can be annotated with multiple reference positions when requested -ok 35 - ngs trained simulator works -ok 36 - ngs trained simulator generates gam -ok -warning[load_proto_to_graph]: dangling edges on missing node 199474497 and 2 other missing nodes removed -[algorithms::normalize] iteration 1 current length 162 -[algorithms::normalize] iteration 2 current length 154 -[algorithms::normalize] iteration 3 current length 154 -[algorithms::normalize] normalized in 2 steps -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -graph: valid -[algorithms::normalize] iteration 1 current length 162 -[algorithms::normalize] iteration 2 current length 154 -[algorithms::normalize] iteration 3 current length 154 -[algorithms::normalize] normalized in 2 steps -graph: valid -graph: valid -[algorithms::normalize] iteration 1 current length 162 -[algorithms::normalize] iteration 2 current length 154 -[algorithms::normalize] iteration 3 current length 154 -[algorithms::normalize] normalized in 2 steps -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -[algorithms::normalize] iteration 1 current length 95 -[algorithms::normalize] iteration 2 current length 95 -[algorithms::normalize] normalized in 1 steps -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -graph: valid - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -graph: valid - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -graph: valid -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -[algorithms::normalize] iteration 1 current length 100 -[algorithms::normalize] iteration 2 current length 100 -[algorithms::normalize] normalized in 1 steps -graph: valid -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -[algorithms::normalize] iteration 1 current length 100 -[algorithms::normalize] iteration 2 current length 100 -[algorithms::normalize] normalized in 1 steps - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 100, which is longer than the non-chunked limit of 16. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 70, which is longer than the non-chunked limit of 16. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -graph: valid -[algorithms::normalize] iteration 1 current length 5 -[algorithms::normalize] normalized in 0 steps -graph: valid -[algorithms::normalize] iteration 1 current length 5 -[algorithms::normalize] normalized in 0 steps -graph: valid - -WARNING:[vg] Subcommand ' -kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - - -WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - - - -WARNING:[vg] Subcommand 'WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely.kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - - - - -WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -graph: valid - - -WARNING:[vg] Subcommand 'kmersWARNING:[vg] Subcommand '' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely.kmers -' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - - - -WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -graph: valid -graph: valid - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 200, which is longer than the non-chunked limit of 19. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 19. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -[algorithms::normalize] iteration 1 current length 106 -[algorithms::normalize] iteration 2 current length 105 -[algorithms::normalize] iteration 3 current length 105 -[algorithms::normalize] normalized in 2 steps -warning: Thread 0 encountered sequence of length 200, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -[algorithms::normalize] iteration 1 current length 103 -[algorithms::normalize] iteration 2 current length 100 -[algorithms::normalize] iteration 3 current length 100 -[algorithms::normalize] normalized in 2 steps -t/14_vg_mod.t ......... -1..32 -ok 1 - vg mod yields a graph with only a particular path -ok 2 - orphan edge removal is automatic -ok 3 - graph complexity reduction works as expected -ok 4 - short subgraph pruning works -ok 5 - normalization produces the correct number of nodes -ok 6 - normalization removes redundant SNP alleles -ok 7 - normalization produces a valid graph -ok 8 - looped normalization produces a valid graph -ok 9 - unchop produces a valid graph -ok 10 - normalization removes redundant sequence in the graph -ok 11 - normalization doesn't introduce cycles and does remove redundancy in bubbles -ok 12 - vg mod removes non-path nodes and edge -ok 13 - chopping a graph works correctly with reverse mappings -ok 14 - unchop correctly handles paths -ok 15 - unchop correctly handles a graph with an inversion -ok 16 - unchop handles doubly-reversing edges -ok 17 - normalization works on a graph with an inversion -ok 18 - mod successfully unchops a difficult graph -ok 19 - chopping self-cycling nodes retains the cycle -ok 20 - unrolling works and produces a valid graph -ok 21 - unfolding works and produces a valid graph -ok 22 - dagify-unroll produces a graph with the same kmers as the original graph -ok 23 - unfold produces a graph with the same kmers as the original graph -ok 24 - dagify handles a graph with two strongly connected components -ok 25 - unfold followed by dagify produces a graph with no cycles -ok 26 - unfold followed by dagify produces a graph with the same kmers as the original graph -ok 27 - dagify unrolls the un-unrollable graph -ok 28 - sibling simplification does not disrupt paths -ok 29 - dagify correctly calculates the minimum distance through the unrolled component -ok 30 - dagify produces a graph of the correct size -ok 31 - subsetting a flat-alleles graph to a sample graph works -ok 32 - removal of high-degree nodes results in the expected number of subgraphs -ok -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -warning:[vg mpmap] It is HIGHLY recommended to use a distance index (-d) for clustering on splice graphs. Both accuracy and speed will suffer without one. -warning:[vg mpmap] It is HIGHLY recommended to use a distance index (-d) for clustering on splice graphs. Both accuracy and speed will suffer without one. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -index file x.sub.fa.fai not found, generating... -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x x.xg -g x.gcsa -n dna --suppress-mismapping -B -G x.gam -i -F GAM -I 60 -D 10 -[vg mpmap] elapsed time 0 s: Loading graph from x.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Loading GCSA2 from x.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Loading LCP from x.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component -[vg mpmap] elapsed time 0 s: Mapping reads from x.gam using 42 threads -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 read pairs. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x x.xg -g x.gcsa -n dna --suppress-mismapping -B -G x.gam -i -F GAMP -I 60 -D 10 -[vg mpmap] elapsed time 0 s: Loading graph from x.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Loading GCSA2 from x.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Loading LCP from x.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component -[vg mpmap] elapsed time 0 s: Mapping reads from x.gam using 42 threads -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 read pairs. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -t/15_vg_surject.t ..... -1..47 -ok 1 - reads are generated -ok 2 - vg surject works perfectly for perfect reads without misaligned homopolymer indels derived from the reference -ok 3 - vg surject works perfectly for perfect reads without misaligned homopolymer indels derived from the reference -ok 4 - vg surject actually places reads on the correct path -ok 5 - vg surject doesn't need to be told which path to use -ok 6 - vg surject reports alignment scores -ok 7 - vg surject picks a reference-sense path if it is present -ok 8 - vg surject works for every read simulated from a dense graph -ok 9 - vg surject spliced algorithm works for every read simulated from a dense graph -ok 10 - vg surject produces valid SAM output -ok 11 - vg map may surject reads to produce valid SAM output -ok 12 - vg map may surject reads to produce valid BAM output -ok 13 - vg surject retains read names -ok 14 - vg surject can set sample and read group -ok 15 - we respect the original mapping's softclips -ok 16 - quality strings we will use for testing are oriented correctly -ok 17 - forward and reverse orientations of a read produce the same surjected SAM, ignoring flags -ok 18 - vg surject produces valid BAM output -ok 19 - mapping quality is preserved through surjection -ok 20 - read pairing is preserved through GAM->GAM surjection -ok 21 - interleaved surjection produces same SAM when using GAF and GAM inputs -ok 22 - surjection of paired reads to SAM yields correct positions -ok 23 - surjection of paired reads to SAM yields correct pair partner positions -ok 24 - surjection of paired reads to SAM yields properly matched QNAMEs -ok 25 - surjection of paired reads to SAM produces correct pair partner contigs -ok 26 - surjection of paired reads to SAM produces correct flags -ok 27 - surjection of paired reads to SAM tags both reads with a read group -ok 28 - surjection of paired reads to SAM creates RG header -ok 29 - surjection works for a longer (151bp) read -ok 30 - surjection works for another difficult read -ok 31 - mapping reproduces qualities from BAM input -ok 32 - mapping reproduces qualities from fastq input -ok 33 - mapping reproduces qualities from GAF input -ok 34 - surject works on GAMP input -ok 35 - surject works on paired GAMP input -ok 36 - vg surject correctly handles subpath suffix in path name -ok 37 - vg surject correctly fetches base path length from input file -ok 38 - vg surject does not crash when surjecting a read that grazes the reference with a deletion -ok 39 - vg surject leaves a read that grazes the reference with a deletion unmapped -ok 40 - vg surject does not crash when surjecting a read that grazes the reference with a deletion and pruning low complexity anchors -ok 41 - vg surject leaves a read that grazes the reference with a deletion unmapped when pruning low complexity anchors -ok 42 - GAM surject can return only primaries -ok 43 - GAM surject can return multimappings -ok 44 - GAM surject can return paired multimappings -ok 45 - GAMP surject can return only primaries -ok 46 - GAMP surject can return multimappings -ok 47 - GAMP surject can return multimappings -ok - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -[algorithms::normalize] iteration 1 current length 1014 -[algorithms::normalize] normalized in 0 steps - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -[algorithms::normalize] iteration 1 current length 1014 -[algorithms::normalize] normalized in 0 steps - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 16. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -[algorithms::normalize] iteration 1 current length 100 -[algorithms::normalize] normalized in 0 steps - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -could not open msgas/t.fa -error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph -error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph -error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -could not open msgas/t.fa -error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph -error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph -error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -[algorithms::normalize] iteration 1 current length 100 -[algorithms::normalize] iteration 2 current length 100 -[algorithms::normalize] normalized in 1 steps - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -index file msgas/s-rev.fa.fai not found, generating... -warning: Thread 0 encountered sequence of length 100, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -[algorithms::normalize] iteration 1 current length 100 -[algorithms::normalize] normalized in 0 steps - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 49, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -graph: valid - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -index file GRCh38_alts/FASTA/HLA/K-3138.fa.fai not found, generating... -warning: Thread 0 encountered sequence of length 3186, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 3186, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 3186, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 3186, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 3184, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 3183, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 3182, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 3181, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -graph: valid - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 200, which is longer than the non-chunked limit of 64. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -graph: valid - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -index file msgas/inv.fa.fai not found, generating... -warning: Thread 0 encountered sequence of length 210, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -[algorithms::normalize] iteration 1 current length 210 -[algorithms::normalize] iteration 2 current length 210 -[algorithms::normalize] normalized in 1 steps - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 70, which is longer than the non-chunked limit of 16. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -graph: valid - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -index file GRCh38_alts/FASTA/HLA/B-3106.fa.fai not found, generating... -warning: Thread 0 encountered sequence of length 3365, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 3364, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 3343, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 3341, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 3341, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 3341, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 3341, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 3340, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -graph: valid - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 210, which is longer than the non-chunked limit of 16. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -graph: valid -t/16_vg_msga.t ........ -1..14 -ok 1 - MSGA produces the expected graph for GRCh38 HLA-V -ok 2 - X-drop DP MSGA produces the expected graph for GRCh38 HLA-V -{"edge": [{"from": "7", "from_start": true, "to": "8", "to_end": true}, {"from": "1", "to": "8"}, {"from": "1", "to": "7"}], "node": [{"id": "7", "sequence": "GGACTAAGGACAAAGGTGCGGGGAG"}, {"id": "8", "sequence": "AACTACTCCACATCAAAGCTACCCAGGCCATTTTAAGTTTCCTGT"}, {"id": "1", "sequence": "TCAGATTCTCATCCCTCCTCAAGGGCTTCT"}], "path": [{"mapping": [{"edit": [{"from_length": 30, "to_length": 30}], "position": {"node_id": "1"}, "rank": "1"}, {"edit": [{"from_length": 45, "to_length": 45}], "position": {"node_id": "8"}, "rank": "2"}, {"edit": [{"from_length": 25, "to_length": 25}], "position": {"node_id": "7"}, "rank": "3"}], "name": "s1"}, {"mapping": [{"edit": [{"from_length": 30, "to_length": 30}], "position": {"node_id": "1"}, "rank": "1"}, {"edit": [{"from_length": 25, "to_length": 25}], "position": {"node_id": "7"}, "rank": "2"}], "name": "s2"}]} -ok 3 - soft clips at node boundaries (start) are included correctly -ok 4 - soft clips at node boundaries (end) are included correctly -ok 5 - region hints (-p) produce same graph -ok 6 - adding in existing sequences in reverse doesn't change graph -ok 7 - the paths of the graph encode the original sequences used to build it -ok 8 - even when banding the paths of the graph encode the original sequences used to build it -ok 9 - HLA K-3138 correctly includes all input paths -ok 10 - a difficult cyclic path can be included to produce a valid graph -ok 11 - a reference sequence set representing an inversion in it may be msga'd and detected -ok 12 - edges in cycles with two nodes are correctly included -ok 13 - HLA B-3106 is assembled into a valid graph -ok 14 - odd-sized overlaps may be used for chunked alignment -ok -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -[vg augment] warning: -a / --augmentation-mode option is deprecated -[vg augment] warning: -a / --augmentation-mode option is deprecated -[vg augment] warning: -a / --augmentation-mode option is deprecated -[vg augment] warning: -a / --augmentation-mode option is deprecated -[vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes -[vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes -[vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes - warning: when streaming in a GAM with -A, the output GAM will lose all non-Path related fields from the input -[vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes -[vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes -[vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -[vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. -[vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. -[vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes -[vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes -[vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes -[vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes -[vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes -[vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes -[vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes -[vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes -[vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes -[vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes -[vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes -[vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes -t/17_vg_augment.t ..... -1..39 -ok 1 - direct augmentation embeds reads fully for well-supported SNPs -ok 2 - adding a well-supported SNP by direct augmentation adds 3 more nodes -ok 3 - adding a well-supported SNP by direct augmentation adds 3 more nodes with -m 1 -ok 4 - direct augmentation embeds with GAF reads fully for well-supported SNPs -ok 5 - adding a well-supported SNP by direct augmentation with GAF adds 3 more nodes -ok 6 - direct augmentation embeds reads fully for probable errors -ok 7 - adding a probable error by direct augmentation adds 3 more nodes -ok 8 - path inclusion does not modify the graph when alignment is a perfect match -ok 9 - path inclusion does not modify the graph when alignment has a SNP but doesnt meet the coverage threshold -ok 10 - path inclusion does not modify the included path when alignment has a SNP but doesnt meet the coverage threshold -ok 11 - output GAM has single edit when SNP was filtered out due to coverage -ok 12 - path inclusion with a complex variant introduces the right number of nodes -ok 13 - path inclusion works for deletions -ok 14 - SNPs can be included in the graph -ok 15 - a soft clip at read start becomes a new head of the graph -ok 16 - a soft clip at read end becomes a new tail of the graph -ok 17 - augment -s works as desired -ok 18 - the expected graph translation is exported when the graph is edited -ok 19 - editing the graph with many SNP-containing alignments does not introduce duplicate identical nodes -ok 20 - augmenting 2 snps with -m 1 produces the same nodes as default -ok 21 - augmenting 2 snps and 2 errors with -m 11 produces the same nodes as with just the snps -ok 22 - augmenting with 2snps makes correct number of nodes -ok 23 - low-quality snp is filtered -ok 24 - augmenting a packed graph produces same results as a vg graph -ok 25 - augmenting a hash graph produces same results as a vg graph -ok 26 - augmenting between nodes without filters works as expected -ok 27 - augmenting between nodes with inactive filters works as expected -ok 28 - augmenting between nodes N filter works as expected -ok 29 - augmenting between nodes without filters works as expected on reverse strand -ok 30 - augmenting between nodes with inactive filters works as expected on reverse strand -ok 31 - augmenting between nodes N filter works as expected on reverse strand -ok 32 - augmenting within node without filters works as expected -ok 33 - augmenting within node with inactive filters works as expected -ok 34 - augmenting within node with N filter works as expected -ok 35 - augmenting within node without filters works as expected on reverse strand -ok 36 - augmenting within node with inactive filters works as expected on reverse strand -ok 37 - augmenting within node with N filter works as expected on reverse strand -ok 38 - sequence in filtered alignment has removed insertion -ok 39 - sequence in filtered alignment has removed insertion on reverse strand -ok -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -index file inverting/miniFasta.fa.fai not found, generating... - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 200, which is longer than the non-chunked limit of 64. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -index file m.fa.fai not found, generating... -[vg autoindex] Executing command: vg autoindex -r small/x.fa -v small/x.vcf.gz -w giraffe -p x -[IndexRegistry]: Checking for phasing in VCF(s). -[IndexRegistry]: Chunking inputs for parallelism. -[IndexRegistry]: Constructing VG graph from FASTA and VCF input. -[IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. -[IndexRegistry]: Stripping allele paths from VG. -[IndexRegistry]: Constructing XG graph from VG graph. -[IndexRegistry]: Downsampling full GBWT. -[IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. -[IndexRegistry]: Constructing GBZ. -[IndexRegistry]: Constructing distance index for Giraffe. -[IndexRegistry]: Constructing minimizer index. -index file x_sub1.fa.fai not found, generating... -index file x_sub2.fa.fai not found, generating... -t/18_vg_call.t ........ -1..19 -ok 1 - calling empty gam gives empty VCF -ok 2 - Called microinversion -ok 3 - Called no microinversion with haploid setting -ok 4 - Fewer than 8 differences between called and true SV genotypes -ok 5 - Fewer than 8 differences between called haploid and truncated true SV genotypes -ok 6 - Same number of reference calls with -a as with -v -ok 7 - Calling from extracted traversals by way of GBWT produces same genotypes as calling directly -ok 8 - Fewer than 3 differences between allales called via traversals or directly -ok 9 - call output same on vg as xg -ok 10 - call output same on vg as xg -ok 11 - vg call finds true homozygous variants in a cyclic graph -ok 12 - vg call finds same variants when using gbwt to enumerate traversals -ok 13 - call produces same output with gbwt and gbz -ok 14 - vg call makes currect base path header with subpath input -ok 15 - vg call makes only currect base path header with subpath input -ok 16 - vg call only reports base paths with subpath input -ok 17 - vg call makes currect base path header with subpath input and override -ok 18 - vg call makes only currect base path header with subpath input and override -ok 19 - overriding contig length does not change calls -ok -t/19_vg_compare.t ..... skipped: (no reason given) -rapper: Parsing file with parser turtle and base URI http://example.org/vg -rapper: Parsing returned 85 triples -rapper: Parsing file with parser turtle and base URI http://example.org/vg -rapper: Parsing returned 75 triples -t/20_vgtordf.t ........ -1..6 -ok 1 - vg view produces the expected number of lines of turtle -ok 2 - vg view produces the expected number of lines of turtle -ok 3 - rapper passed -ok 4 - rapper passed -ok 5 - vg view produces the expected number of lines of turtle -ok 6 - vg view produces the expected number of lines of turtle -ok -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x g.xg -g g.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -I 10 -D 50 -F GAM -t 1 -[vg mpmap] elapsed time 0 s: Loading graph from g.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Loading GCSA2 from g.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Loading LCP from g.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component -[vg mpmap] elapsed time 0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x g.xg -g g.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -I 10 -D 1 -F GAM -t 1 -[vg mpmap] elapsed time 0 s: Loading graph from g.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Loading GCSA2 from g.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Loading LCP from g.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component -[vg mpmap] elapsed time 0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. -t/21_vg_filter.t ...... -1..13 -ok 1 - vg filter with no options preserves input. -ok 2 - vg filter downsamples correctly -ok 3 - samtools 1.0+ and vg filter agree on how to select downsampled paired reads -ok 4 - samtools 1.0+ and vg filter agree on how to select downsampled unpaired reads -ok 5 - reads with refpos annotations not matching an exclusion regex are let through -ok 6 - reads with refpos annotations matching an exclusion regex are removed -ok 7 - negating a non-filter results in no reads -ok 8 - a filter and its complement should form the entire file -ok 9 - properly paired read passes proper filter -ok 10 - improperly paired read fails proper filter -ok 11 - read pairs can be tropped by feature -ok 12 - read pairs can be kept if only one read fails -ok 13 - unmapped reads can be filtered out -ok -t/22_ggsv.t ........... skipped: (no reason given) -t/23_vectorize.t ...... skipped: (no reason given) -[vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. -t/25_circularize.t .... -1..2 -ok 1 - a path may be circularized -ok 2 - a circular path survives a round trip to/from xg -ok - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -[algorithms::normalize] iteration 1 current length 1014 -[algorithms::normalize] normalized in 0 steps -Warning [vg deconstruct]: -e is deprecated as it's now on default -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -Warning [vg deconstruct]: -e is deprecated as it's now on default -Warning [vg deconstruct]: -e is deprecated as it's now on default -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -Warning [vg deconstruct]: -e is deprecated as it's now on default -Warning [vg deconstruct]: -e is deprecated as it's now on default -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -Warning [vg deconstruct]: -e is deprecated as it's now on default -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -Warning [vg deconstruct]: -H is deprecated, and will be ignored -Warning [vg deconstruct]: -e is deprecated as it's now on default -Warning [vg deconstruct]: -d is deprecated - ploidy now inferred from haplotypes in path names -Warning [vg deconstruct]: -H is deprecated, and will be ignored -Warning [vg deconstruct]: -e is deprecated as it's now on default -Warning [vg deconstruct]: -d is deprecated - ploidy now inferred from haplotypes in path names -t/26_deconstruct.t: line 127: bcftools: command not found -t/26_deconstruct.t: line 128: bcftools: command not found -t/26_deconstruct.t: line 129: bcftools: command not found -t/26_deconstruct.t: line 130: bcftools: command not found -[vg autoindex] Executing command: vg autoindex -r small/x.fa -v small/x.vcf.gz -w giraffe -p x -[IndexRegistry]: Checking for phasing in VCF(s). -[IndexRegistry]: Chunking inputs for parallelism. -[IndexRegistry]: Constructing VG graph from FASTA and VCF input. -[IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. -[IndexRegistry]: Stripping allele paths from VG. -[IndexRegistry]: Constructing XG graph from VG graph. -[IndexRegistry]: Downsampling full GBWT. -[IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. -[IndexRegistry]: Constructing GBZ. -[IndexRegistry]: Constructing distance index for Giraffe. -[IndexRegistry]: Constructing minimizer index. -t/26_deconstruct.t .... -1..37 -ok 1 - deconstructed hla vcf has correct number of sites -ok 2 - deconstructed hla vcf has correct insertion -ok 3 - deconstructed hla vcf with other path has correct number of sites -ok 4 - deconstructed hla vcf has correct deletion -ok 5 - path-based and exhaustive decontruction give equivalent sites when expected -ok 6 - path that differs from reference in every alt has correct genotype -ok 7 - path that is same as reference in every alt has correct genotype -ok 8 - reference contig correctly written -ok 9 - deconstruct correctly handles a simple inversion -ok 10 - deconstruct correctly handles a simple inversion when the reference contains the reversing edge -ok 11 - deconstruct applies translation from gbz with -O -ok 12 - deconstruct correctly handles a cycle in the reference path when contained inside snarl -ok 13 - deconstruct correctly handles a cycle in the alt path -ok 14 - cyclic reference deconstruction has correct number of variants -ok 15 - deconstruct correctly handles cycle in the reference path that spans snarl -ok 16 - -P -H options return correct number of variants -ok 17 - -P -H options use correct reference name -ok 18 - -P -H does not find conflict in alt1 in second variant -ok 19 - deconstructing vg graph gives same output as xg graph -ok 20 - haplotype 1 preserved when deconstructing small test with gbwt -ok 21 - haplotype 2 preserved when deconstructing small test with gbwt -ok 22 - gbz deconstruction gives same output as gbwt deconstruction -ok 23 - cluster-free deconstruction finds all alt alleles -ok 24 - clustered deconstruction finds fewer alt alleles -ok 25 - clustered deconstruction finds correct allele info -ok 26 - nested deconstruction gets correct star-allele for snp inside deletion -ok 27 - PA=0 correctly set at both sites of neseted deletion -ok 28 - nested deconstruction gets correct allele for snp inside deletion (without -R) -ok 29 - nested deconstruction gets correct allele for snp inside insert -ok 30 - PA=0 set for base allele of nested insertion -ok 31 - PA=1 set for nested allele of nested insertion -ok 32 - nested deconstruction gets correct contigs in vcf header for snp inside insert -ok 33 - nested deconstruction gets correct star allele for snp ins2.ide ins2.ert -ok 34 - INFO tags correct for level-0 site of double-nested SNP -ok 35 - INFO tags correct for level-1 site of double-nested SNP -ok 36 - INFO tags correct for level-2 site of double-nested SNP -ok 37 - nested deconstruction handles cycle -ok -Statistics: -Number of Non-Degenerate Snarls: 4 -Snarls traversed by reads: 4 -Snarls on reference: 0 -Snarl length distribution: -Statistics: -Number of Non-Degenerate Snarls: 4 -Snarls traversed by reads: 4 -Snarls on reference: 4 -Snarl length distribution: -2 1 -1 3 -index file flat1.fa.fai not found, generating... -index file flat2.fa.fai not found, generating... -Statistics: -Number of Non-Degenerate Snarls: 8 -Snarls traversed by reads: 8 -Snarls on reference: 0 -Snarl length distribution: - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -index file flats.fa.fai not found, generating... -Warning: realigned read TATGTCTGTAGG doesn't touch either end of its snarl! -Warning: realigned read CCCTACAGACAT doesn't touch either end of its snarl! -Warning: realigned read GAGCCCTACAGA doesn't touch either end of its snarl! -Warning: realigned read CTCATTGTAACG doesn't touch either end of its snarl! -Warning: realigned read CTGTAGGGCTCA doesn't touch either end of its snarl! -Warning: realigned read GGGCTCATTGTA doesn't touch either end of its snarl! -Warning: realigned read AGGGCTCATTGT doesn't touch either end of its snarl! -Warning: realigned read CCTACAGACATA doesn't touch either end of its snarl! -Warning: realigned read GCTCATTGTAAC doesn't touch either end of its snarl! -Warning: realigned read TTACAATGAGCC doesn't touch either end of its snarl! -Warning: realigned read TACAGACATATC doesn't touch either end of its snarl! -Warning: realigned read CTGTAGGGCTCA doesn't touch either end of its snarl! -Warning: realigned read TAGGGCTCATTG doesn't touch either end of its snarl! -Warning: realigned read GTTACAATGAGC doesn't touch either end of its snarl! -Warning: realigned read TACAATGAGCCC doesn't touch either end of its snarl! -Warning: realigned read GTCTGTAGGGCT doesn't touch either end of its snarl! -Warning: realigned read TGTCTGTAGGGC doesn't touch either end of its snarl! -Warning: realigned read TGAGCCCTACAG doesn't touch either end of its snarl! -Warning: realigned read TACAATGAGCCC doesn't touch either end of its snarl! -Warning: realigned read ACGTTACAATGA doesn't touch either end of its snarl! -Warning: realigned read GCTCATTGTAAC doesn't touch either end of its snarl! -Warning: realigned read GCCCTACAGACA doesn't touch either end of its snarl! -Warning: realigned read TGTCTGTAGGGC doesn't touch either end of its snarl! -Warning: realigned read ACGTTACAATGA doesn't touch either end of its snarl! -Warning: realigned read GTAGGGCTCATT doesn't touch either end of its snarl! -Statistics: -Number of Non-Degenerate Snarls: 1 -Snarls traversed by reads: 1 -Snarls on reference: 1 -Snarl length distribution: -0 1 -t/27_vg_genotype.t .... -1..5 -ok 1 - vg genotype runs successfully -ok 2 - vg genotype runs successfully when emitting vcf -ok 3 - called genotypes are correct in a small simulated example -ok 4 - genotype format can be converted to and from JSON -ok 5 - genotype finds big insert -ok - -WARNING:[vg] Subcommand 'translate' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -[algorithms::normalize] iteration 1 current length 57 -[algorithms::normalize] normalized in 0 steps -[algorithms::normalize] iteration 1 current length 57 -[algorithms::normalize] normalized in 0 steps - -WARNING:[vg] Subcommand 'translate' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - - -WARNING:[vg] Subcommand 'translate' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -t/28_translate.t ...... -1..2 -ok 1 - alignments used to modify a graph may be projected back to the original graph and used to regenerate the same graph -ok 2 - translation overlay works and produces a sane result -ok -[vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. -warning[vg chunk]: the vg-protobuf format is DEPRECATED. you probably want to use PackedGraph (pg) instead -[vg] warning: node ID 44 appears multiple times. Skipping. -[vg] warning: node ID 45 appears multiple times. Skipping. -[vg] warning: node ID 43 appears multiple times. Skipping. -[vg] warning: edge 43 end <-> 44 start appears multiple times. Skipping. -[vg] warning: edge 43 end <-> 45 start appears multiple times. Skipping. -[vg] warning: node ID 87 appears multiple times. Skipping. -[vg] warning: node ID 88 appears multiple times. Skipping. -[vg] warning: node ID 85 appears multiple times. Skipping. -[vg] warning: node ID 86 appears multiple times. Skipping. -[vg] warning: edge 87 end <-> 88 start appears multiple times. Skipping. -[vg] warning: edge 85 end <-> 87 start appears multiple times. Skipping. -[vg] warning: edge 85 end <-> 86 start appears multiple times. Skipping. -[vg] warning: edge 86 end <-> 88 start appears multiple times. Skipping. -[vg] warning: node ID 130 appears multiple times. Skipping. -[vg] warning: node ID 131 appears multiple times. Skipping. -[vg] warning: node ID 129 appears multiple times. Skipping. -[vg] warning: edge 130 end <-> 131 start appears multiple times. Skipping. -[vg] warning: edge 129 end <-> 130 start appears multiple times. Skipping. -[vg] warning: edge 129 end <-> 131 start appears multiple times. Skipping. -[vg] warning: node ID 173 appears multiple times. Skipping. -[vg] warning: node ID 174 appears multiple times. Skipping. -[vg] warning: node ID 172 appears multiple times. Skipping. -[vg] warning: edge 173 end <-> 174 start appears multiple times. Skipping. -[vg] warning: edge 172 end <-> 173 start appears multiple times. Skipping. -[vg] warning: edge 172 end <-> 174 start appears multiple times. Skipping. -Restricting to x from 1 to end -Restricting to y from 1 to end -[vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. -[vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. -t/30_vg_chunk.t ....... -1..32 -ok 1 - vg chunk with no options preserves nodes -ok 2 - vg chunk with no options preserves edges -ok 3 - chunk has path going through node 9 -ok 4 - chunk can be found from GBZ -ok 5 - snarl chunk works on simple example -ok 6 - chunk has path going through node 9 -ok 7 - -s produces correct number of chunks -ok 8 - gam chunker produces correct number of graphs -ok 9 - gam chunker produces correct number of gams -ok 10 - gam chunker produces bed with correct number of chunks -ok 11 - gam chunker emits each matching read at most once -ok 12 - chunk contains the expected number of alignments -ok 13 - simple gam chunker produces correct number of gams -ok 14 - simple chunk contains the expected number of alignments -ok 15 - id chunker produces correct chunk size -ok 16 - id chunker produces correct single chunk -ok 17 - id chunker traces correct chunk size without haplotypes -ok 18 - id chunker traces correct chunk size -ok 19 - chunker extracts no threads from an empty gPBWT -ok 20 - chunker extracts 2 local threads from a gBWT with 2 locally distinct threads in it -ok 21 - chunker can extract a partial haplotype from a GBWT -ok 22 - chunker can extract a partial haplotype from a GBZ -ok 23 - chunker doesn't see haplotypes in the GBZ if asked not to -ok 24 - trace consistent on path coordinates -ok 25 - n-chunking works and chunks over the full graph -ok 26 - path-based components finds subgraphs -ok 27 - x gam chunk has correct number of reads -ok 28 - y gam chunk has correct number of reads -ok 29 - x gam chunk has correct number of reads with -p path -ok 30 - y gam chunk has correct number of reads with -p path -ok 31 - path-based component contains correct path length -ok 32 - components finds subgraphs -ok -index file add/ref.fa.fai not found, generating... - -WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -Variant 1: 3 haplotypes at ref:18: 32 bp vs. 33 bp haplotypes vs. graphs average -Variant 2: 3 haplotypes at ref:21: 32 bp vs. 34 bp haplotypes vs. graphs average -Variant 3: 3 haplotypes at ref:23: 33 bp vs. 34 bp haplotypes vs. graphs average - -WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -Variant 1: 3 haplotypes at chrR:18: 32 bp vs. 33 bp haplotypes vs. graphs average -Variant 2: 3 haplotypes at chrR:21: 32 bp vs. 34 bp haplotypes vs. graphs average -Variant 3: 3 haplotypes at chrR:23: 33 bp vs. 34 bp haplotypes vs. graphs average - -WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -Variant 1: 3 haplotypes at ref:18: 32 bp vs. 33 bp haplotypes vs. graphs average -Variant 2: 3 haplotypes at ref:21: 32 bp vs. 34 bp haplotypes vs. graphs average -Variant 3: 3 haplotypes at ref:23: 33 bp vs. 34 bp haplotypes vs. graphs average - -WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -Variant 1: 4 haplotypes at ref:2: 33 bp vs. 34 bp haplotypes vs. graphs average -Variant 2: 4 haplotypes at ref:21: 33 bp vs. 36 bp haplotypes vs. graphs average -Variant 3: 4 haplotypes at ref:32: 33 bp vs. 36 bp haplotypes vs. graphs average -index file add/refN.fa.fai not found, generating... - -WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -Variant 1: 4 haplotypes at ref:2: 33 bp vs. 34 bp haplotypes vs. graphs average -Variant 2: 4 haplotypes at ref:21: 33 bp vs. 36 bp haplotypes vs. graphs average -Variant 3: 4 haplotypes at ref:32: 33 bp vs. 36 bp haplotypes vs. graphs average -index file add/ngap.fa.fai not found, generating... - -WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -Variant 1: 2 haplotypes at ngap:10923: 224 bp vs. 224 bp haplotypes vs. graphs average -Variant 2: 5 haplotypes at ngap:11014: 256 bp vs. 258 bp haplotypes vs. graphs average -Variant 3: 5 haplotypes at ngap:11030: 256 bp vs. 261 bp haplotypes vs. graphs average -Variant 4: 5 haplotypes at ngap:11035: 256 bp vs. 261 bp haplotypes vs. graphs average -Variant 5: 5 haplotypes at ngap:11043: 256 bp vs. 261 bp haplotypes vs. graphs average - -WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -Variant 1: 2 haplotypes at x:9: 160 bp vs. 161 bp haplotypes vs. graphs average -Variant 2: 2 haplotypes at x:10: 160 bp vs. 167 bp haplotypes vs. graphs average -Variant 3: 2 haplotypes at x:14: 160 bp vs. 167 bp haplotypes vs. graphs average -Variant 4: 2 haplotypes at x:34: 160 bp vs. 167 bp haplotypes vs. graphs average -Variant 5: 2 haplotypes at x:39: 160 bp vs. 167 bp haplotypes vs. graphs average -Variant 6: 2 haplotypes at x:52: 224 bp vs. 231 bp haplotypes vs. graphs average -Variant 7: 2 haplotypes at x:58: 224 bp vs. 232 bp haplotypes vs. graphs average -Variant 8: 2 haplotypes at x:100: 256 bp vs. 265 bp haplotypes vs. graphs average -Variant 9: 2 haplotypes at x:103: 256 bp vs. 267 bp haplotypes vs. graphs average -Variant 10: 2 haplotypes at x:122: 288 bp vs. 299 bp haplotypes vs. graphs average -Variant 11: 2 haplotypes at x:142: 288 bp vs. 301 bp haplotypes vs. graphs average -Variant 12: 2 haplotypes at x:160: 306 bp vs. 319 bp haplotypes vs. graphs average -Variant 13: 2 haplotypes at x:172: 338 bp vs. 353 bp haplotypes vs. graphs average -Variant 14: 2 haplotypes at x:178: 313 bp vs. 327 bp haplotypes vs. graphs average -Variant 15: 2 haplotypes at x:187: 313 bp vs. 327 bp haplotypes vs. graphs average -Variant 16: 2 haplotypes at x:200: 294 bp vs. 306 bp haplotypes vs. graphs average -Variant 17: 2 haplotypes at x:204: 294 bp vs. 306 bp haplotypes vs. graphs average -Variant 18: 2 haplotypes at x:218: 288 bp vs. 300 bp haplotypes vs. graphs average -Variant 19: 2 haplotypes at x:221: 288 bp vs. 300 bp haplotypes vs. graphs average -Variant 20: 2 haplotypes at x:272: 256 bp vs. 266 bp haplotypes vs. graphs average -Variant 21: 2 haplotypes at x:277: 256 bp vs. 272 bp haplotypes vs. graphs average -Variant 22: 2 haplotypes at x:287: 256 bp vs. 272 bp haplotypes vs. graphs average -Variant 23: 2 haplotypes at x:294: 256 bp vs. 272 bp haplotypes vs. graphs average -Variant 24: 2 haplotypes at x:297: 291 bp vs. 305 bp haplotypes vs. graphs average -Variant 25: 2 haplotypes at x:312: 323 bp vs. 340 bp haplotypes vs. graphs average -Variant 26: 2 haplotypes at x:313: 323 bp vs. 341 bp haplotypes vs. graphs average -Variant 27: 2 haplotypes at x:345: 291 bp vs. 306 bp haplotypes vs. graphs average -Variant 28: 2 haplotypes at x:347: 323 bp vs. 339 bp haplotypes vs. graphs average -Variant 29: 2 haplotypes at x:353: 311 bp vs. 326 bp haplotypes vs. graphs average -Variant 30: 2 haplotypes at x:373: 291 bp vs. 306 bp haplotypes vs. graphs average -Variant 31: 2 haplotypes at x:397: 288 bp vs. 307 bp haplotypes vs. graphs average -Variant 32: 2 haplotypes at x:398: 288 bp vs. 307 bp haplotypes vs. graphs average -Variant 33: 2 haplotypes at x:405: 241 bp vs. 258 bp haplotypes vs. graphs average -Variant 34: 2 haplotypes at x:408: 241 bp vs. 258 bp haplotypes vs. graphs average -Variant 35: 2 haplotypes at x:466: 254 bp vs. 260 bp haplotypes vs. graphs average -Variant 36: 2 haplotypes at x:474: 286 bp vs. 295 bp haplotypes vs. graphs average -Variant 37: 2 haplotypes at x:489: 286 bp vs. 296 bp haplotypes vs. graphs average -Variant 38: 2 haplotypes at x:500: 286 bp vs. 297 bp haplotypes vs. graphs average -Variant 39: 2 haplotypes at x:523: 300 bp vs. 309 bp haplotypes vs. graphs average -Variant 40: 2 haplotypes at x:533: 289 bp vs. 299 bp haplotypes vs. graphs average -Variant 41: 1 haplotypes at x:553: 257 bp vs. 263 bp haplotypes vs. graphs average -Variant 42: 1 haplotypes at x:566: 257 bp vs. 263 bp haplotypes vs. graphs average -Variant 43: 2 haplotypes at x:629: 277 bp vs. 281 bp haplotypes vs. graphs average -Variant 44: 2 haplotypes at x:647: 278 bp vs. 285 bp haplotypes vs. graphs average -Variant 45: 2 haplotypes at x:654: 278 bp vs. 287 bp haplotypes vs. graphs average -Variant 46: 2 haplotypes at x:668: 310 bp vs. 320 bp haplotypes vs. graphs average -Variant 47: 2 haplotypes at x:669: 310 bp vs. 321 bp haplotypes vs. graphs average -Variant 48: 2 haplotypes at x:681: 289 bp vs. 299 bp haplotypes vs. graphs average -Variant 49: 2 haplotypes at x:688: 289 bp vs. 299 bp haplotypes vs. graphs average -Variant 50: 2 haplotypes at x:698: 280 bp vs. 289 bp haplotypes vs. graphs average -Variant 51: 2 haplotypes at x:714: 299 bp vs. 307 bp haplotypes vs. graphs average -Variant 52: 2 haplotypes at x:757: 287 bp vs. 299 bp haplotypes vs. graphs average -Variant 53: 2 haplotypes at x:775: 273 bp vs. 285 bp haplotypes vs. graphs average -Variant 54: 2 haplotypes at x:777: 273 bp vs. 286 bp haplotypes vs. graphs average -Variant 55: 2 haplotypes at x:789: 273 bp vs. 287 bp haplotypes vs. graphs average -Variant 56: 2 haplotypes at x:795: 273 bp vs. 287 bp haplotypes vs. graphs average -Variant 57: 2 haplotypes at x:813: 287 bp vs. 300 bp haplotypes vs. graphs average -Variant 58: 2 haplotypes at x:823: 287 bp vs. 302 bp haplotypes vs. graphs average -Variant 59: 2 haplotypes at x:827: 319 bp vs. 334 bp haplotypes vs. graphs average -Variant 60: 2 haplotypes at x:858: 297 bp vs. 310 bp haplotypes vs. graphs average -Variant 61: 2 haplotypes at x:859: 297 bp vs. 312 bp haplotypes vs. graphs average -Variant 62: 2 haplotypes at x:860: 297 bp vs. 312 bp haplotypes vs. graphs average -Variant 63: 2 haplotypes at x:877: 287 bp vs. 303 bp haplotypes vs. graphs average -Variant 64: 2 haplotypes at x:888: 244 bp vs. 262 bp haplotypes vs. graphs average -Variant 65: 2 haplotypes at x:899: 243 bp vs. 263 bp haplotypes vs. graphs average -Variant 66: 2 haplotypes at x:901: 243 bp vs. 264 bp haplotypes vs. graphs average -Variant 67: 2 haplotypes at x:916: 224 bp vs. 243 bp haplotypes vs. graphs average -Variant 68: 2 haplotypes at x:917: 224 bp vs. 243 bp haplotypes vs. graphs average -Variant 69: 2 haplotypes at x:923: 223 bp vs. 243 bp haplotypes vs. graphs average -Variant 70: 2 haplotypes at x:925: 223 bp vs. 243 bp haplotypes vs. graphs average -Variant 71: 2 haplotypes at x:929: 222 bp vs. 242 bp haplotypes vs. graphs average -Variant 72: 2 haplotypes at x:939: 204 bp vs. 223 bp haplotypes vs. graphs average -Variant 73: 2 haplotypes at x:945: 204 bp vs. 223 bp haplotypes vs. graphs average -Variant 74: 2 haplotypes at x:972: 177 bp vs. 194 bp haplotypes vs. graphs average -Variant 75: 2 haplotypes at x:1000: 136 bp vs. 149 bp haplotypes vs. graphs average - -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead.WARNING:[vg] Subcommand ' -add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -Variant 1: 3 haplotypes at ref:18: 32 bp vs. 33 bp haplotypes vs. graphs average -Variant 2: 3 haplotypes at ref:21: 32 bp vs. 34 bp haplotypes vs. graphs average -Variant 3: 3 haplotypes at ref:23: 33 bp vs. 34 bp haplotypes vs. graphs average - -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead.WARNING:[vg] Subcommand ' -add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -Variant 1: 3 haplotypes at ref:18: 32 bp vs. 33 bp haplotypes vs. graphs average -Variant 2: 3 haplotypes at ref:21: 32 bp vs. 34 bp haplotypes vs. graphs average -Variant 3: 3 haplotypes at ref:23: 33 bp vs. 34 bp haplotypes vs. graphs average -Variant 4: 3 haplotypes at ref3:18: 32 bp vs. 34 bp haplotypes vs. graphs average -Variant 5: 3 haplotypes at ref3:21: 32 bp vs. 34 bp haplotypes vs. graphs average -Variant 6: 3 haplotypes at ref3:23: 33 bp vs. 34 bp haplotypes vs. graphs average - -WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -Variant 1: 3 haplotypes at ref:18: 32 bp vs. 33 bp haplotypes vs. graphs average -Variant 2: 3 haplotypes at ref:21: 32 bp vs. 34 bp haplotypes vs. graphs average -Variant 3: 3 haplotypes at ref:23: 33 bp vs. 34 bp haplotypes vs. graphs average -t/31_vg_add.t ......... -1..12 -ok 1 - vg add can create a graph -ok 2 - vg add can create a graph with contig renames -ok 3 - vg add produces the same graph from VCFs with different contig names -ok 4 - vg add can create a graph from a PackedGraph -ok 5 - vg add produces the same graph from the same input in different formats -ok 6 - having reference Ns does not affect the graph topology -ok 7 - adding variants adds only the alt bases near large N gaps -ok 8 - vg add can create a slightly larger graph -ok 9 - ranks are calculated for emitted paths -ok 10 - graphs with backward nodes can be added to -ok 11 - graphs with multiple overlapping paths nodes can be added to -ok 12 - graphs with backward and forward nodes can be added to -ok -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -Restricting to x from 1 to end -Restricting to y from 1 to end -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -[vg autoindex] Executing command: vg autoindex -p index -g graphs/big_snarl_named.gfa -w giraffe -[IndexRegistry]: Checking for haplotype lines in GFA. -[IndexRegistry]: Constructing VG graph from GFA input. -[IndexRegistry]: Constructing XG graph from VG graph. -[IndexRegistry]: Constructing a greedy path cover GBWT -[IndexRegistry]: Constructing GBZ using NamedNodeBackTranslation. -[IndexRegistry]: Constructing distance index for Giraffe. -[IndexRegistry]: Constructing minimizer index. -t/32_vg_snarls.t ...... -1..19 -ok 1 - vg snarls made right number of protobuf Snarls -ok 2 - vg snarls made right number of protobuf SnarlTraversals -ok 3 - vg snarls made snarls in the right order -ok 4 - vg snarls on xg made right number of protobuf Snarls -ok 5 - vg snarls on xg made right number of protobuf SnarlTraversals -ok 6 - vcf traversals are the same as exhaustive traversals for tiny graph -ok 7 - vcf traversals are the same as exhaustive traversals for inversion -ok 8 - vcf traversals are the same as exhaustive traversals for ins_and_del graph -ok 9 - correct number of snarls when parallelizing on compoents -ok 10 - same number of snarls when parallelizing on components -ok 11 - GBZ graphs can be used for finding snarls -ok 12 - correct number of snarls in the GFA W-line example -ok 13 - vg snarls made the right snarls when dealing with nested chains -ok 14 - vg snarls made snarls in the right order when dealing with nested chains -ok 15 - Correct snarls are found in GFA space -ok 16 - In node ID space traversal visits 7 nodes -ok 17 - In node ID space traversal visits 4 trivial snarls -ok 18 - In segment name space traversal visits 3 segments -ok 19 - In segment name space traversal visits 0 trivial snarls -ok -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap --suppress-mismapping -B -P 1 -n dna -x xy2.xg -g xy2.gcsa -f reads/xy2.match.fq -F GAM -[vg mpmap] elapsed time 0 s: Loading graph from xy2.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component -[vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.match.fq using 42 threads -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap --suppress-mismapping -B -P 1 -n dna -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -f reads/xy2.match.fq -F GAM -[vg mpmap] elapsed time 0 s: Loading graph from xy2.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Loading GBWT from xy2.gbwt -[vg mpmap] elapsed time 0 s: Completed loading GBWT -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component -[vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.match.fq using 42 threads -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. -warning:[vg mpmap] It is HIGHLY recommended to use a distance index (-d) for clustering on splice graphs. Both accuracy and speed will suffer without one. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap --suppress-mismapping -B -M 2 -n rna -x xy2.xg -g xy2.gcsa -f reads/xy2.match.fq -[vg mpmap] elapsed time 0 s: Loading graph from xy2.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Identifying reference paths -[vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component -[vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.match.fq using 42 threads -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -I 200 -D 200 -x xy2.xg -g xy2.gcsa -f reads/xy2.matchpaired.fq -i -F GAM -t 1 -[vg mpmap] elapsed time 0 s: Loading graph from xy2.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component -[vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.matchpaired.fq using 1 thread -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -I 200 -D 200 -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -f reads/xy2.matchpaired.fq -i -F GAM -t 1 -[vg mpmap] elapsed time 0 s: Loading graph from xy2.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Loading GBWT from xy2.gbwt -[vg mpmap] elapsed time 0 s: Completed loading GBWT -[vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component -[vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.matchpaired.fq using 1 thread -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. -warning:[vg mpmap] Snarl file (-s) is ignored for single path alignment formats (-F) without multipath population scoring (--max-paths). -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -x xy2.xg -g xy2.gcsa -s xy2.snarls -f reads/xy2.discordant.fq -F GAM -t 1 -[vg mpmap] elapsed time 0 s: Loading graph from xy2.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component -[vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.discordant.fq using 1 thread -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. -warning:[vg mpmap] Snarl file (-s) is ignored for single path alignment formats (-F) without multipath population scoring (--max-paths). -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -x xy2.xg -g xy2.gcsa -s xy2.snarls -f reads/xy2.discordant.fq -F GAM -t 1 -[vg mpmap] elapsed time 0 s: Loading graph from xy2.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component -[vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.discordant.fq using 1 thread -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -s xy2.snarls -f reads/xy2.discordant.fq -t 1 -F GAM -[vg mpmap] elapsed time 0 s: Loading graph from xy2.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Loading snarls from xy2.snarls -[vg mpmap] elapsed time 0 s: Completed loading snarls -[vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Loading GBWT from xy2.gbwt -[vg mpmap] elapsed time 0 s: Completed loading GBWT -[vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component -[vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.discordant.fq using 1 thread -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -s xy2.snarls -f reads/xy2.discordant.fq -t 1 -F GAM -[vg mpmap] elapsed time 0 s: Loading graph from xy2.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Loading snarls from xy2.snarls -[vg mpmap] elapsed time 0 s: Completed loading snarls -[vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Loading GBWT from xy2.gbwt -[vg mpmap] elapsed time 0 s: Completed loading GBWT -[vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component -[vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.discordant.fq using 1 thread -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -I 10 -D 50 -F GAM -t 1 -[vg mpmap] elapsed time 0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component -[vg mpmap] elapsed time 0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -I 100000 -D 5 -F GAM -t 1 -[vg mpmap] elapsed time 0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component -[vg mpmap] elapsed time 0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -F GAM -t 1 -[vg mpmap] elapsed time 0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component -[vg mpmap] elapsed time 0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread -warning:[vg mpmap] Could not find 1000 (-b) unambiguous read pair mappings to estimate fragment length ditribution. This can happen due to data issues (e.g. unpaired reads being mapped as pairs) or because the sample size is too large for the read set. Mapping read pairs as independent single-ended reads. -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -G input.gam -I 500 -D 100 -n dna -i -F GAM --no-qual-adjust -[vg mpmap] elapsed time 0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component -[vg mpmap] elapsed time 0 s: Mapping reads from input.gam using 42 threads -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1000 read pairs. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -n dna -x t.xg -g t.gcsa -f t.fq -[vg mpmap] elapsed time 0 s: Loading graph from t.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Loading GCSA2 from t.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Loading LCP from t.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component -[vg mpmap] elapsed time 1 s: Mapping reads from t.fq using 42 threads -[vg mpmap] elapsed time 1 s: Mapping finished. Mapped 3 reads. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq -[vg mpmap] elapsed time 0 s: Loading graph from s.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Identifying reference paths -[vg mpmap] elapsed time 0 s: Loading GCSA2 from s.gcsa -[vg mpmap] elapsed time 0 s: Loading distance index from s.dist (in background) -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Loading LCP from s.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Completed loading distance index -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Mapping reads from s.fq using 42 threads -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq -i -I 350 -D 10 -[vg mpmap] elapsed time 0 s: Loading graph from s.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Identifying reference paths -[vg mpmap] elapsed time 0 s: Loading GCSA2 from s.gcsa -[vg mpmap] elapsed time 0 s: Loading distance index from s.dist (in background) -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Completed loading distance index -[vg mpmap] elapsed time 0 s: Loading LCP from s.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 1 s: Mapping reads from s.fq using 42 threads -[vg mpmap] elapsed time 1 s: Mapping finished. Mapped 1 read pairs. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq -i -I 530 -D 10 -[vg mpmap] elapsed time 0 s: Loading graph from s.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Identifying reference paths -[vg mpmap] elapsed time 0 s: Loading GCSA2 from s.gcsa -[vg mpmap] elapsed time 0 s: Loading distance index from s.dist (in background) -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Completed loading distance index -[vg mpmap] elapsed time 0 s: Loading LCP from s.gcsa.lcp -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Mapping reads from s.fq using 42 threads -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq -i -I 530 -D 10 -F SAM --report-group-mapq -[vg mpmap] elapsed time 0 s: Loading graph from s.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Identifying reference paths -[vg mpmap] elapsed time 0 s: Loading GCSA2 from s.gcsa -[vg mpmap] elapsed time 0 s: Loading distance index from s.dist (in background) -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Completed loading distance index -[vg mpmap] elapsed time 0 s: Loading LCP from s.gcsa.lcp -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: No reference path file given. Interpreting all non-alt-allele paths in graph as reference sequences. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -[vg mpmap] elapsed time 0 s: Mapping reads from s.fq using 42 threads -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x xy.xg -d xy.dist -g xy.gcsa -G x.gam -F SAM -i --frag-mean 50 --frag-stddev 10 -M 1 -[vg mpmap] elapsed time 0 s: Loading graph from xy.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Identifying reference paths -[vg mpmap] elapsed time 0 s: Loading GCSA2 from xy.gcsa -[vg mpmap] elapsed time 0 s: Loading distance index from xy.dist (in background) -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Completed loading distance index -[vg mpmap] elapsed time 0 s: Loading LCP from xy.gcsa.lcp -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: No reference path file given. Interpreting all non-alt-allele paths in graph as reference sequences. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -[vg mpmap] elapsed time 0 s: Building null model to calibrate mismapping detection -[vg mpmap] elapsed time 8 s: Mapping reads from x.gam using 42 threads -[vg mpmap] elapsed time 8 s: Mapping finished. Mapped 1000 read pairs. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x xy.xg -d xy.dist -g xy.gcsa -G x.gam -F SAM -M 1 -[vg mpmap] elapsed time 0 s: Loading graph from xy.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Identifying reference paths -[vg mpmap] elapsed time 0 s: Loading GCSA2 from xy.gcsa -[vg mpmap] elapsed time 0 s: Loading distance index from xy.dist (in background) -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Completed loading distance index -[vg mpmap] elapsed time 0 s: Loading LCP from xy.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: No reference path file given. Interpreting all non-alt-allele paths in graph as reference sequences. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -[vg mpmap] elapsed time 0 s: Building null model to calibrate mismapping detection -[vg mpmap] elapsed time 10 s: Mapping reads from x.gam using 42 threads -[vg mpmap] elapsed time 10 s: Mapping finished. Mapped 2000 reads. -t/33_vg_mpmap.t ....... -1..21 -ok 1 - MAPQ is 50% without haplotype info -ok 2 - haplotype match can disambiguate -ok 3 - MAPQs are computed for all multimappings -ok 4 - MAPQ is 50% when paired without haplotype info -ok 5 - haplotype match can disambiguate paired -ok 6 - use of haplotype-aware mapping is recorded -ok 7 - Haplotype-oblivious mapping places read on the wrong contig -ok 8 - Haplotype-oblivious mapping places read with MAPQ of 50% -ok 9 - Haplotype-aware mapping places read on the right contig -ok 10 - Haplotype-aware mapping places read with MAPQ > 50% -ok 11 - paired read alignments forced to be consistent have lower score than unrestricted alignments -ok 12 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments -ok 13 - paired read alignments forced to be near each other are closer together in node id space than those forced to be far apart -ok 14 - small batches are still all paired in the output -ok 15 - multipath mapping works in scenarios that trigger branch point trimming -ok 16 - spliced alignments can be found when aligning RNA -ok 17 - paired mapping can identify a splice junction on read 1 -ok 18 - paired mapping can identify a splice junction on read 2 -ok 19 - HTS output contains group mapq annotation -ok 20 - paired reads are evenly split between equivalent mappings -ok 21 - unpaired reads are evenly split between equivalent mappings -ok -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -t/34_vg_pack.t ........ -1..20 -ok 1 - allele observation packing detects 2 SNPs -ok 2 - pileup packs agree with graph coverage -ok 3 - graph coverages are merged from multiple .cx indexes -ok 4 - edit records are merged from multiple .cx indexes -ok 5 - binned edit accumulation does not affect the result -ok 6 - pack records are filtered by node id -ok 7 - pack records are filtered by node id -ok 8 - pack index merging produces the expected result -ok 9 - pack index merging produces the expected result for edges -ok 10 - pack computes the same total edge coverage as pileup -ok 11 - pack stores the correct edge pileup to disk -ok 12 - node packs on vg same as xg -ok 13 - edge packs on vg same as xg -ok 14 - node packs same on vg when using 3 threads as when using 1 -ok 15 - edge packs same on vg when using 2 threads as when using 1 -ok 16 - node packs on gaf same as gam -ok 17 - edge packs on gaf same as gam -ok 18 - average node qualities are correct -ok 19 - pack -s 10 sets fist and last 10bp of coverage to 0 like expected -ok 20 - pack -s 9 sets fist and last 9bp of coverage to 0 like expected -ok -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. -t/36_vg_annotate.t .... -1..9 -ok 1 - we can detect when reads contain non-reference variation -ok 2 - vg annotate finds the right number of reads overlapping a feature -ok 3 - all reads overlapping a feature fall on its node -ok 4 - vg annotate finds no reads touching both of two distant features -ok 5 - vg annotate shows reads having to go through one feature to get to another at the end -ok 6 - vg annotate shows all reads overlapping a whole-reference-covering feature -ok 7 - annotating with earliest path position produces one position -ok 8 - annotating with multiple path positions produces multiple positions -ok 9 - annotations derived from BED can span the end/start joins of circular paths -ok -t/37_vg_gbwt.t ........ -1..159 -ok 1 - chromosome X GBWT with vg gbwt -ok 2 - chromosome X GBWT with vg index -ok 3 - identical construction results with vg gbwt and vg index -ok 4 - chromosome X VCF parse -ok 5 - chromosome X GBWT from VCF parse -ok 6 - identical construction results with vg gbwt and from VCF parse -ok 7 - chromosome X: 2 threads -ok 8 - chromosome X: 1 contig -ok 9 - chromosome X: 2 haplotypes -ok 10 - chromosome X: 1 sample -ok 11 - chromosome X: 2 thread names -ok 12 - chromosome X: 1 contig name -ok 13 - chromosome X: 1 sample name -ok 14 - chromosome X reference GBWT with vg gbwt -ok 15 - chromosome X reference GBWT with vg index -ok 16 - identical construction results with vg gbwt and vg index -ok 17 - chromosome X reference: 1 thread -ok 18 - chromosome X GAF with vg gbwt -ok 19 - chromosome X GAF with vg index -ok 20 - identical construction results with vg gbwt and vg index -ok 21 - chromosome X GAM with vg gbwt -ok 22 - identical construction results from GAF and GAM -ok 23 - chromosome X subgraph GBWT with vg gbwt -ok 24 - no warnings about missing variants -ok 25 - chromosome X subgraph GBWT with vg index -ok 26 - identical construction results with vg gbwt and vg index -ok 27 - insertion merging with multiple chromosomes -ok 28 - fast merging with multiple chromosomes -ok 29 - identical merging results with the insertion and fast algorithms -ok 30 - parallel merging with multiple chromosomes -ok 31 - identical merging results with the insertion and parallel algorithms -ok 32 - direct construction with multiple chromosomes and a single VCF -ok 33 - identical results with direct construction and merging -ok 34 - direct construction with multiple chromosomes and multiple VCFs -ok 35 - identical construction results with a single VCF and multiple VCFs -ok 36 - construction preset: 1000gp -ok 37 - multiple chromosomes: 4 threads -ok 38 - multiple chromosomes: 2 contigs -ok 39 - multiple chromosomes: 2 haplotypes -ok 40 - multiple chromosomes: 1 sample -ok 41 - paths as contigs with vg gbwt -ok 42 - paths as contigs with vg index -ok 43 - identical construction results with vg gbwt and vg index -ok 44 - paths as contigs: 2 threads -ok 45 - paths as contigs: 2 contigs -ok 46 - paths as contigs: 1 haplotype -ok 47 - paths as contigs: 1 sample -ok 48 - r-index construction -ok 49 - normal merging: non-empty + empty -ok 50 - the index remains unchanged -ok 51 - normal merging: empty + non-empty -ok 52 - the index remains unchanged -ok 53 - fast merging: non-empty + empty -ok 54 - the index remains unchanged -ok 55 - fast merging: empty + non-empty -ok 56 - the index remains unchanged -ok 57 - parallel merging: non-empty + empty -ok 58 - the index remains unchanged -ok 59 - parallel merging: empty + non-empty -ok 60 - the index remains unchanged -ok 61 - haplotypes and paths: 6 threads -ok 62 - samples can be removed from a GBWT index -ok 63 - haplotypes only: 4 threads -ok 64 - all samples: 12 threads -ok 65 - all samples: 6 haplotypes -ok 66 - multiple samples can be removed from a GBWT index -ok 67 - sample 2: 4 threads -ok 68 - sample 2: 2 haplotypes -ok 69 - threads can be extracted from GBWT -ok 70 - correct size for the thread file -ok 71 - GBWTGraph construction -ok 72 - GBWTGraph was serialized correctly -ok 73 - GBZ construction from GBWT -ok 74 - GBZ was serialized correctly -ok 75 - GBZ construction from VCF -ok 76 - Identical construction results from GBWT and VCF -ok 77 - GBZ construction from GBWTGraph -ok 78 - Identical construction results from XG and GBWTGraph -ok 79 - GBWT extraction from GBZ -ok 80 - Identical GBWT indexes -ok 81 - GBWT + GBWTGraph extraction from GBZ -ok 82 - Identical GBWT indexes -ok 83 - Identical GBWTGraphs -ok 84 - Path cover GBWTGraph construction -ok 85 - GBWTGraph was serialized correctly -ok 86 - path cover: 32 threads -ok 87 - path cover: 2 contigs -ok 88 - path cover: 16 haplotypes -ok 89 - path cover: 16 samples -ok 90 - Path cover GBWTGraph construction -ok 91 - GBWTGraph was serialized correctly -ok 92 - path cover w/ paths: 34 threads -ok 93 - path cover w/ paths: 2 contigs -ok 94 - path cover w/ paths: 17 haplotypes -ok 95 - path cover w/ paths: 17 samples -ok 96 - Local haplotypes GBWTGraph construction -ok 97 - GBWTGraph was serialized correctly -ok 98 - local haplotypes: 32 threads -ok 99 - local haplotypes: 2 contigs -ok 100 - local haplotypes: 16 haplotypes -ok 101 - local haplotypes: 16 samples -ok 102 - Local haplotypes GBZ construction (single job) -ok 103 - GBZ was serialized correctly -ok 104 - Local haplotypes GBZ construction (two jobs) -ok 105 - GBZ was serialized correctly -ok 106 - Local haplotypes GBWTGraph construction -ok 107 - GBWTGraph was serialized correctly -ok 108 - local haplotypes w/ paths: 34 threads -ok 109 - local haplotypes w/ paths: 2 contigs -ok 110 - local haplotypes w/ paths: 17 haplotypes -ok 111 - local haplotypes w/ paths: 17 samples -ok 112 - Local haplotypes with reference paths from a larger GBZ -ok 113 - local haplotypes w/ paths: 36 threads -ok 114 - local haplotypes w/ paths: 2 contigs -ok 115 - local haplotypes w/ paths: 18 haplotypes -ok 116 - local haplotypes w/ paths: 18 samples -ok 117 - local haplotypes w/ paths: reference_samples set -ok 118 - Augmented GBWTGraph construction -ok 119 - GBWTGraph was serialized correctly -ok 120 - augmented: 18 threads -ok 121 - augmented: 2 contigs -ok 122 - augmented: 18 haplotypes -ok 123 - augmented: 17 samples -ok 124 - GBWT construction from GFA -ok 125 - GBWT was serialized correctly -ok 126 - gfa: 4 threads -ok 127 - gfa: 2 contigs -ok 128 - gfa: 2 haplotypes -ok 129 - gfa: 1 sample -ok 130 - GBWT+GBWTGraph construction from GFA -ok 131 - Identical construction results with and without GBWTGraph -ok 132 - GBWTGraph was serialized correctly -ok 133 - no chopping: 0 translations -ok 134 - GBZ construction from GFA -ok 135 - GBZ was serialized correctly -ok 136 - GBWT+GBWTGraph construction from GFA with chopping -ok 137 - chopping: 3 threads -ok 138 - chopping: 1 contig -ok 139 - chopping: 3 haplotypes -ok 140 - chopping: 2 samples -ok 141 - chopping: 9 translations -ok 142 - Translation can be extracted from GBZ -ok 143 - from GBZ: 8 translations -ok 144 - GBWT+GBWTGraph construction from GFA with reference paths -ok 145 - ref paths: 6 threads -ok 146 - ref paths: 2 contigs -ok 147 - ref paths: 3 haplotypes -ok 148 - ref paths: 2 samples -ok 149 - ref paths: 0 translations -ok 150 - GBZ construction from GFA with reference -ok 151 - GBZ GBWT tag extraction works -ok 152 - GBWT tags contain the correct reference samples -ok 153 - GBZ GBWT tag modification works -ok 154 - Changing reference_samples tag can make a reference a haplotype -ok 155 - Changing reference_samples tag can make a haplotype a reference -ok 156 - GBZ GBWT tag modification validation works -ok 157 - Samples can be direcly set as references -ok 158 - Direct reference assignment works -ok 159 - GBZ can represent reference paths without haplotype numbers -ok -t/38_vg_prune.t ....... -1..21 -ok 1 - pruning produces the correct number of components -ok 2 - pruning leaves the correct number of nodes -ok 3 - pruning leaves the correct number of edges -ok 4 - pruning without high-degree nodes produces the correct number of components -ok 5 - pruning without high-degree nodes leaves the correct number of nodes -ok 6 - pruning without high-degree nodes leaves the correct number of edges -ok 7 - pruning with path restoring produces the correct number of components -ok 8 - pruning with path restoring leaves the correct number of nodes -ok 9 - pruning with path restoring leaves the correct number of edges -ok 10 - pruning with path/thread unfolding produces the correct number of components -ok 11 - pruning with path/thread unfolding produces the correct number of nodes -ok 12 - pruning with path/thread unfolding produces the correct number of edges -ok 13 - pruning with path unfolding produces the correct number of components -ok 14 - pruning with path unfolding produces the correct number of nodes -ok 15 - pruning with path unfolding produces the correct number of edges -ok 16 - unfolding with multi-chromosome GBWT produces the correct number of components -ok 17 - unfolding with multi-chromosome GBWT produces the correct number of nodes -ok 18 - unfolding with multi-chromosome GBWT produces the correct number of edges -ok 19 - empty mapping starts from the right node id -ok 20 - the first unfolded graph adds the correct number of nodes to the mapping -ok 21 - the second unfolded graph adds the correct number of nodes to the mapping -ok -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -t/39_vg_inject.t ...... -1..14 -ok 1 - reads are generated -ok 2 - vg inject works for all reads included in the original bam -ok 3 - vg inject retains read names -ok 4 - vg inject works perfectly for the position of alignment in the simple graph -ok 5 - vg inject works perfectly for the position of alignment -ok 6 - vg inject works perfectly for the mapping quality of alignment -ok 7 - vg inject works perfectly for the cigar of alignment in the simple graph -ok 8 - vg inject works perfectly for the cigar of alignment -ok 9 - vg inject preserves all reads +not ok 7 - vg inject works perfectly for the cigar of alignment in the simple graph +# got: '100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 19M1D81M +# 24M1I75M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 62M1D32M1D6M +# 100M +# 100M +# 60M1I39M +# 100M +# 100M +# 60M1D40M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 52M1D42M1I5M +# 14M1D86M +# 19M1I80M +# 100M +# 100M +# 100M +# 79M1D21M +# 100M +# 100M +# 100M +# 100M +# 100M +# 9M1I90M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 56M1D22M1I21M +# 100M +# 100M +# 100M +# 29M1I70M +# 100M +# 34M1I65M +# 16M1D84M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 75M1I24M +# 100M +# 100M +# 73M1D27M +# 100M +# 100M +# 52M1D48M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 21M1I78M +# 100M +# 100M +# 3M1D97M +# 100M +# 100M +# 8M1D92M +# 100M +# 67M1I32M +# 48M1D52M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 78M1D22M +# 100M +# 100M +# 100M +# 100M +# 15M1D85M +# 94M1I5M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 10M1I89M +# 100M +# 100M +# 100M +# 100M +# 100M +# 22M1I77M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 26M1D74M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 12M1I64M1D23M +# 100M +# 100M +# 100M +# 28M1I71M +# 5M1I94M +# 100M +# 100M +# 100M +# 100M +# 3M1D97M +# 83M1D10M1I6M +# 80M1D20M +# 100M +# 100M +# 100M +# 100M +# 100M +# 79M1D10M1I10M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 7M1I92M +# 100M +# 39M1I60M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 3M1D64M1I32M +# 59M1I40M +# 100M +# 100M +# 100M +# 100M +# 60M1I39M +# 63M1I36M +# 100M +# 29M1D43M1D28M +# 100M +# 100M +# 100M +# 33M1D67M +# 100M +# 100M +# 100M +# 100M +# 55M1I44M +# 100M +# 100M +# 100M +# 46M1D54M +# 100M +# 100M +# 100M +# 100M +# 8M1I91M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 58M1I41M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 36M1D64M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 85M1I14M +# 100M +# 86M1I13M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 39M1D61M +# 100M +# 86M1D14M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 67M1I32M +# 100M +# 61M1D39M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 17M1D26M1D57M +# 100M +# 100M +# 100M +# 100M +# 100M +# 4M1I95M +# 100M +# 100M +# 100M +# 35M1I64M +# 100M +# 13M1I86M +# 100M +# 46M1D54M +# 44M1I55M +# 74M1I25M +# 100M +# 100M +# 100M +# 8M1D19M1I72M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 84M1D16M +# 100M +# 100M +# 100M +# 100M +# 100M +# 64M1D36M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 57M1D43M +# 14M1D86M +# 100M +# 100M +# 28M1I71M +# 100M +# 100M +# 100M +# 31M1I68M +# 100M +# 100M +# 100M +# 86M1D14M +# 100M +# 45M1I54M +# 100M +# 100M +# 100M +# 100M +# 86M1I13M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 91M1I8M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 35M1I64M +# 100M +# 100M +# 100M +# 56M1D44M +# 100M +# 13M1D45M1D42M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 39M1D61M +# 100M +# 100M +# 100M +# 15M1D85M +# 100M +# 100M +# 100M +# 42M1D58M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 41M1I58M +# 100M +# 100M +# 100M +# 100M +# 24M1D76M +# 49M1D51M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 48M1D52M +# 68M1D32M +# 39M1D51M1D10M +# 100M +# 100M +# 100M +# 9M1D91M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 68M1D32M +# 100M +# 100M +# 100M +# 50M1I49M +# 100M +# 100M +# 100M +# 63M1I17M1I18M +# 5M1D95M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 9M1I90M +# 100M +# 40M1I59M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 72M1I27M +# 100M +# 100M +# 100M +# 100M +# 100M +# 61M1I38M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 85M1I14M +# 100M +# 100M +# 93M1D7M +# 100M +# 100M +# 43M1I9M1I46M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 82M1D18M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 61M1I38M +# 49M1I50M +# 100M +# 100M +# 100M +# 100M +# 28M1D72M +# 100M +# 100M +# 23M1I76M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 68M1I6M1I24M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 45M1D55M +# 100M +# 43M1I39M1I16M +# 100M +# 93M1D7M +# 66M1I33M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 58M1D42M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 64M1D36M +# 100M +# 100M +# 59M1D41M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 66M1D34M +# 94M1D6M +# 100M +# 100M +# 100M +# 46M1I53M +# 100M +# 48M1D52M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 50M1D50M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 57M1D13M1D18M1D12M +# 84M1D16M +# 61M1D39M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 28M1D72M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 86M1D14M +# 100M +# 100M +# 100M +# 95M5S +# 100M +# 100M +# 100M +# 100M +# 22M1D78M +# 100M +# 100M +# 100M +# 2S98M +# 100M +# 100M +# 95M1I4M +# 100M +# 95M1D5M +# 100M +# 76M1D24M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 5M1D69M1D26M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 86M1I13M +# 100M +# 100M +# 65M1I34M +# 100M +# 100M +# 100M +# 100M +# 100M +# 18M1D82M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 37M1I62M +# 100M +# 100M +# 100M +# 67M1I32M +# 100M +# 100M +# 100M +# 100M +# 100M +# 58M1I41M +# 28M1I71M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 4M1D96M +# 69M1I30M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 16M1I32M1D51M +# 100M +# 100M +# 100M +# 84M1I15M +# 100M +# 100M +# 12M1D88M +# 100M +# 35M1I64M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 49M1D51M +# 100M +# 100M +# 100M +# 100M +# 14M1D86M +# 68M1D32M +# 27M1D73M +# 100M +# 100M +# 71M1I28M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 90M1D10M +# 100M +# 100M +# 35M1D65M +# 100M +# 4M1I61M1I33M +# 100M +# 100M +# 100M +# 100M +# 9M1D91M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 66M1I33M +# 100M +# 50M1I49M +# 100M +# 100M +# 100M +# 100M +# 100M +# 38M1I52M1I8M +# 100M +# 100M +# 100M +# 45M1I54M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 7M1I92M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 27M1I72M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 84M1D16M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 37M1D63M +# 100M +# 100M +# 43M1D18M1I38M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 68M1D32M +# 88M1D12M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 8M1D24M1I67M +# 88M1D12M +# 100M +# 100M +# 100M +# 50M1I49M +# 44M1D56M +# 100M +# 56M1D44M +# 100M +# 34M1I65M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 49M1D51M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 42M1D58M +# 35M1I64M +# 100M +# 100M +# 100M +# 100M +# 24M1D76M +# 76M1I23M +# 100M +# 100M +# 68M1I31M +# 100M +# 100M +# 6M1I93M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 34M1D66M +# 31M1D69M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 15M1I84M +# 100M +# 100M +# 100M +# 5M1I94M +# 100M +# 100M +# 100M +# 100M +# 100M +# 50M1D50M +# 100M +# 100M +# 64M1D36M +# 100M +# 96M1D4M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 25M1D75M +# 85M1I14M +# 48M1D52M +# 100M +# 100M +# 21M1D79M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 9M1I90M +# 100M +# 100M +# 100M +# 100M +# 100M +# 90M1D10M +# 100M' +# expected: '' +not ok 8 - vg inject works perfectly for the cigar of alignment +# got: '100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 19M1D81M +# 24M1I75M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 62M1D32M1D6M +# 100M +# 100M +# 60M1I39M +# 100M +# 100M +# 60M1D40M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 52M1D42M1I5M +# 14M1D86M +# 19M1I80M +# 100M +# 100M +# 100M +# 79M1D21M +# 100M +# 100M +# 100M +# 100M +# 100M +# 9M1I90M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 56M1D22M1I21M +# 100M +# 100M +# 100M +# 29M1I70M +# 100M +# 34M1I65M +# 16M1D84M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 75M1I24M +# 100M +# 100M +# 73M1D27M +# 100M +# 100M +# 52M1D48M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 21M1I78M +# 100M +# 100M +# 3M1D97M +# 100M +# 100M +# 8M1D92M +# 100M +# 67M1I32M +# 48M1D52M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 78M1D22M +# 100M +# 100M +# 100M +# 100M +# 15M1D85M +# 94M1I5M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 10M1I89M +# 100M +# 100M +# 100M +# 100M +# 100M +# 22M1I77M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 26M1D74M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 12M1I64M1D23M +# 100M +# 100M +# 100M +# 28M1I71M +# 5M1I94M +# 100M +# 100M +# 100M +# 100M +# 3M1D97M +# 83M1D10M1I6M +# 80M1D20M +# 100M +# 100M +# 100M +# 100M +# 100M +# 79M1D10M1I10M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 7M1I92M +# 100M +# 39M1I60M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 3M1D64M1I32M +# 59M1I40M +# 100M +# 100M +# 100M +# 100M +# 60M1I39M +# 63M1I36M +# 100M +# 29M1D43M1D28M +# 100M +# 100M +# 100M +# 33M1D67M +# 100M +# 100M +# 100M +# 100M +# 55M1I44M +# 100M +# 100M +# 100M +# 46M1D54M +# 100M +# 100M +# 100M +# 100M +# 8M1I91M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 58M1I41M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 36M1D64M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 85M1I14M +# 100M +# 86M1I13M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 39M1D61M +# 100M +# 86M1D14M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 67M1I32M +# 100M +# 61M1D39M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 17M1D26M1D57M +# 100M +# 100M +# 100M +# 100M +# 100M +# 4M1I95M +# 100M +# 100M +# 100M +# 35M1I64M +# 100M +# 13M1I86M +# 100M +# 46M1D54M +# 44M1I55M +# 74M1I25M +# 100M +# 100M +# 100M +# 8M1D19M1I72M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 84M1D16M +# 100M +# 100M +# 100M +# 100M +# 100M +# 64M1D36M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 57M1D43M +# 14M1D86M +# 100M +# 100M +# 28M1I71M +# 100M +# 100M +# 100M +# 31M1I68M +# 100M +# 100M +# 100M +# 86M1D14M +# 100M +# 45M1I54M +# 100M +# 100M +# 100M +# 100M +# 86M1I13M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 91M1I8M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 35M1I64M +# 100M +# 100M +# 100M +# 56M1D44M +# 100M +# 13M1D45M1D42M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 39M1D61M +# 100M +# 100M +# 100M +# 15M1D85M +# 100M +# 100M +# 100M +# 42M1D58M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 41M1I58M +# 100M +# 100M +# 100M +# 100M +# 24M1D76M +# 49M1D51M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 48M1D52M +# 68M1D32M +# 39M1D51M1D10M +# 100M +# 100M +# 100M +# 9M1D91M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 68M1D32M +# 100M +# 100M +# 100M +# 50M1I49M +# 100M +# 100M +# 100M +# 63M1I17M1I18M +# 5M1D95M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 9M1I90M +# 100M +# 40M1I59M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 72M1I27M +# 100M +# 100M +# 100M +# 100M +# 100M +# 61M1I38M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 85M1I14M +# 100M +# 100M +# 93M1D7M +# 100M +# 100M +# 43M1I9M1I46M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 82M1D18M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 61M1I38M +# 49M1I50M +# 100M +# 100M +# 100M +# 100M +# 28M1D72M +# 100M +# 100M +# 23M1I76M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 68M1I6M1I24M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 45M1D55M +# 100M +# 43M1I39M1I16M +# 100M +# 93M1D7M +# 66M1I33M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 58M1D42M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 64M1D36M +# 100M +# 100M +# 59M1D41M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 66M1D34M +# 94M1D6M +# 100M +# 100M +# 100M +# 46M1I53M +# 100M +# 48M1D52M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 50M1D50M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 57M1D13M1D18M1D12M +# 84M1D16M +# 61M1D39M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 28M1D72M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 86M1D14M +# 100M +# 100M +# 100M +# 95M5S +# 100M +# 100M +# 100M +# 100M +# 22M1D78M +# 100M +# 100M +# 100M +# 2S98M +# 100M +# 100M +# 95M1I4M +# 100M +# 95M1D5M +# 100M +# 76M1D24M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 5M1D69M1D26M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 86M1I13M +# 100M +# 100M +# 65M1I34M +# 100M +# 100M +# 100M +# 100M +# 100M +# 18M1D82M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 37M1I62M +# 100M +# 100M +# 100M +# 67M1I32M +# 100M +# 100M +# 100M +# 100M +# 100M +# 58M1I41M +# 28M1I71M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 4M1D96M +# 69M1I30M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 16M1I32M1D51M +# 100M +# 100M +# 100M +# 84M1I15M +# 100M +# 100M +# 12M1D88M +# 100M +# 35M1I64M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 49M1D51M +# 100M +# 100M +# 100M +# 100M +# 14M1D86M +# 68M1D32M +# 27M1D73M +# 100M +# 100M +# 71M1I28M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 90M1D10M +# 100M +# 100M +# 35M1D65M +# 100M +# 4M1I61M1I33M +# 100M +# 100M +# 100M +# 100M +# 9M1D91M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 66M1I33M +# 100M +# 50M1I49M +# 100M +# 100M +# 100M +# 100M +# 100M +# 38M1I52M1I8M +# 100M +# 100M +# 100M +# 45M1I54M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 7M1I92M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 27M1I72M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 84M1D16M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 37M1D63M +# 100M +# 100M +# 43M1D18M1I38M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 68M1D32M +# 88M1D12M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 8M1D24M1I67M +# 88M1D12M +# 100M +# 100M +# 100M +# 50M1I49M +# 44M1D56M +# 100M +# 56M1D44M +# 100M +# 34M1I65M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 49M1D51M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 42M1D58M +# 35M1I64M +# 100M +# 100M +# 100M +# 100M +# 24M1D76M +# 76M1I23M +# 100M +# 100M +# 68M1I31M +# 100M +# 100M +# 6M1I93M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 34M1D66M +# 31M1D69M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 15M1I84M +# 100M +# 100M +# 100M +# 5M1I94M +# 100M +# 100M +# 100M +# 100M +# 100M +# 50M1D50M +# 100M +# 100M +# 64M1D36M +# 100M +# 96M1D4M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 25M1D75M +# 85M1I14M +# 48M1D52M +# 100M +# 100M +# 21M1D79M +# 100M +# 100M +# 100M +# 100M +# 100M +# 100M +# 9M1I90M +# 100M +# 100M +# 100M +# 100M +# 100M +# 90M1D10M +# 100M' +# expected: '' +not ok 9 - vg inject preserves all reads +# got: '0' +# expected: '470' ok 10 - vg inject works perfectly for the reads flagged as is_reverse ok 11 - vg inject does not make an alignment for an umapped read ok 12 - vg inject does not crash on an unmapped read -ok 13 - vg inject supports GAF output +not ok 13 - vg inject supports GAF output +# got: '0' +# expected: '1000' ok 14 - vg inject produces valid alignments of the read and reference -ok -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -1000 reads correct -1 reads correct -1 reads correct -0 reads correct -0 reads correct -1 reads correct +Dubious, test returned 1 (wstat 256, 0x100) +Failed 10/14 subtests +t/40_vg_gamcompare.t: line 11: 3288328 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > s.vg +t/40_vg_gamcompare.t: line 12: 3288329 Illegal instruction vg index -x s.xg -g s.gcsa s.vg +t/40_vg_gamcompare.t: line 13: 3288330 Illegal instruction vg snarls -T s.vg > s.snarls +t/40_vg_gamcompare.t: line 14: 3288331 Illegal instruction vg index -j s.dist s.vg +t/40_vg_gamcompare.t: line 15: 3288332 Illegal instruction vg sim -n 1000 -l 100 -e 0.01 -i 0.005 -x s.xg -a > s.sim +t/40_vg_gamcompare.t: line 22: 3288344 Illegal instruction vg map -x s.xg -g s.gcsa -s "AATCTCTCTGAACTTCAGTTTAATTATC" > read1.gam +t/40_vg_gamcompare.t: line 23: 3288345 Illegal instruction vg annotate -a read1.gam -p -x s.xg > read1.single.gam +t/40_vg_gamcompare.t: line 24: 3288346 Illegal instruction vg annotate -a read1.gam -m -x s.xg > read1.multi.gam +t/40_vg_gamcompare.t: line 25: 3288347 Illegal instruction vg map -x s.xg -g s.gcsa -s "TCTAATATGGAGATGATACTACTGACAG" > read2.gam +t/40_vg_gamcompare.t: line 26: 3288348 Illegal instruction vg annotate -a read2.gam -p -x s.xg > read2.single.gam +t/40_vg_gamcompare.t: line 27: 3288349 Illegal instruction vg annotate -a read2.gam -m -x s.xg > read2.multi.gam t/40_vg_gamcompare.t .. 1..7 -ok 1 - gamcompare completes -ok 2 - gamcompare says the truth is correctly mapped -ok 3 - Reads annotated with leftmost position only are close enough at a long distance -ok 4 - Reads are close enough at a long distance with a distance index +not ok 1 - gamcompare completes +# got: '0' +# expected: '1000' +not ok 2 - gamcompare says the truth is correctly mapped +# got: '0' +# expected: '1000' +not ok 3 - Reads annotated with leftmost position only are close enough at a long distance +# got: '0' +# expected: '1' +not ok 4 - Reads are close enough at a long distance with a distance index +# got: '0' +# expected: '1' ok 5 - Reads annotated with leftmost position only are too far apart at a short distance ok 6 - Reads are too far apart at a short distance with a distance index -ok 7 - Reads annotated with multiple positions only are close enough at a short distance -ok -[Viz::init] error: Image would be 86252x88 which is larger than the maximum 32,767 px on a side canvas that Cairo supports for raster images. Use an SVG output, try `odgi viz`, or reduce your input size! +not ok 7 - Reads annotated with multiple positions only are close enough at a short distance +# got: '0' +# expected: '1' +Failed 5/7 subtests +t/41_vg_viz.t: line 11: 3288378 Illegal instruction vg construct -r tiny/tiny.fa -v tiny/tiny.vcf.gz > t.vg +t/41_vg_viz.t: line 12: 3288379 Illegal instruction vg index -x t.xg -g t.gcsa t.vg +t/41_vg_viz.t: line 13: 3288380 Illegal instruction vg map -G <(vg sim -l 30 -n 100 -x t.xg -a) -d t + 3288381 | vg pack -x t.xg -o t.cx -g - +t/41_vg_viz.t: line 15: 3288383 Illegal instruction vg viz -x t.xg -o t.svg -i t.cx -n alignments +wc: t.svg: No such file or directory +(standard_in) 1: syntax error +t/41_vg_viz.t: line 19: 3288391 Illegal instruction vg viz -x t.xg -o t.png +t/41_vg_viz.t: line 24: 3288393 Illegal instruction vg viz -x graphs/cactus-BRCA2.gfa -o cactus.png t/41_vg_viz.t ......... 1..4 -ok 1 - vg viz runs -ok 2 - vg viz succeeds when drawing a PNG -ok 3 - vg viz actually creates an output PNG -ok 4 - vg viz knows when a graph is too big to draw as a PNG -ok +not ok 1 - unnamed test +# got: '1' +# expected: 'vg viz runs' +not ok 2 - vg viz succeeds when drawing a PNG +# got: '132' +# expected: '0' +not ok 3 - vg viz actually creates an output PNG +# got: '1' +# expected: '0' +not ok 4 - vg viz knows when a graph is too big to draw as a PNG +# got: '132' +# expected: '1' +Failed 4/4 subtests +t/42_vg_gamsort.t: line 11: 3288396 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > x.vg +t/42_vg_gamsort.t: line 12: 3288397 Illegal instruction vg index -x x.xg x.vg +t/42_vg_gamsort.t: line 13: 3288398 Illegal instruction vg sim -n 1000 -l 100 -e 0.01 -i 0.005 -x x.xg -a > x.gam +t/42_vg_gamsort.t: line 15: 3288399 Illegal instruction vg gamsort x.gam > x.sorted.gam +t/42_vg_gamsort.t: line 22: 3288409 Illegal instruction vg gamsort x.gam -i x.sorted.gam.gai > x.sorted.gam t/42_vg_gamsort.t ..... 1..2 ok 1 - Sorting a GAM orders the alignments by min node ID -ok 2 - sorted GAMs can be indexed during the sort -ok -graph: valid +not ok 2 - sorted GAMs can be indexed during the sort +# got: '132' +# expected: '0' +Failed 1/2 subtests +t/43_vg_simplify.t: line 10: 3288412 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz -a > x.vg +t/43_vg_simplify.t: line 13: 3288413 Illegal instruction vg simplify --algorithm small x.vg > x.small.vg 2> /dev/null +t/43_vg_simplify.t: line 18: 3288418 Illegal instruction vg simplify --algorithm rare --min-count 2 -v small/x.vcf.gz x.vg > x.rare.vg +t/43_vg_simplify.t: line 21: 3288419 Illegal instruction vg validate x.rare.vg t/43_vg_simplify.t .... 1..5 -ok 1 - vg simplify runs through when popping small bubbles -ok 2 - simplification pops all the bubbles in a simple graph -ok 3 - vg simplify runs through when removing rare variants -ok 4 - the graph is valid after removing rare variants -ok 5 - simplification keeps only some variants -ok +not ok 1 - vg simplify runs through when popping small bubbles +# got: '132' +# expected: '0' +not ok 2 - simplification pops all the bubbles in a simple graph +# got: '' +# expected: '1' +not ok 3 - vg simplify runs through when removing rare variants +# got: '132' +# expected: '0' +not ok 4 - the graph is valid after removing rare variants +# got: '132' +# expected: '0' +not ok 5 - simplification keeps only some variants +# got: '' +# expected: '118' +Failed 5/5 subtests +t/44_vg_benchmark.t: line 10: 3288426 Illegal instruction vg benchmark > /dev/null t/44_vg_benchmark.t ... 1..1 -ok 1 - vg benchmark completes succesfully -ok - -WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - - -WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - - -WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - - -WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - +not ok 1 - vg benchmark completes succesfully +# got: '132' +# expected: '0' +Failed 1/1 subtests +t/45_vg_sort.t: line 12: 3288428 Illegal instruction vg construct -r minigiab/q.fa -v minigiab/NA12878.chr22.tiny.giab.vcf.gz -m 64 + 3288429 | vg mod -X 1 - > giab.vg +t/45_vg_sort.t: line 21: 3288434 Illegal instruction vg sort -a id -I giab.sorted.vg.vgi giab.vg > giab.sorted.vg +t/45_vg_sort.t: line 25: 3288435 Illegal instruction vg sort -a topo giab.vg > /dev/null +t/45_vg_sort.t: line 28: 3288436 Illegal instruction vg sort -a eades -r q giab.vg > /dev/null +t/45_vg_sort.t: line 31: 3288437 Illegal instruction vg sort -a max-flow -r q giab.vg > /dev/null t/45_vg_sort.t ........ 1..5 -ok 1 - ids in our test graph are not initially in sorted order -ok 2 - a vg graph can be sorted and indexed by ID without crashing -ok 3 - a vg graph can be sorted topologically -ok 4 - a vg graph can be sorted with Eades algorithm without crashing -ok 5 - a vg graph can be sorted with the max-flow algorithm without crashing -ok +not ok 1 - ids in our test graph are not initially in sorted order +# got: '0' +# expected: '1' +not ok 2 - a vg graph can be sorted and indexed by ID without crashing +# got: '132' +# expected: '0' +not ok 3 - a vg graph can be sorted topologically +# got: '132' +# expected: '0' +not ok 4 - a vg graph can be sorted with Eades algorithm without crashing +# got: '132' +# expected: '0' +not ok 5 - a vg graph can be sorted with the max-flow algorithm without crashing +# got: '132' +# expected: '0' +Failed 5/5 subtests +t/46_vg_minimizer.t: line 12: 3288440 Illegal instruction vg construct -r small/xy.fa -v small/xy2.vcf.gz -R x -C -a > x.vg 2> /dev/null +t/46_vg_minimizer.t: line 13: 3288441 Illegal instruction vg index -x x.xg x.vg +t/46_vg_minimizer.t: line 14: 3288442 Illegal instruction vg gbwt -x x.vg -o x.gbwt -v small/xy2.vcf.gz +t/46_vg_minimizer.t: line 15: 3288443 Illegal instruction vg index -j x.dist x.xg +t/46_vg_minimizer.t: line 18: 3288444 Illegal instruction vg minimizer --no-dist -o x.mi -g x.gbwt x.xg +t/46_vg_minimizer.t: line 22: 3288445 Illegal instruction vg minimizer -o x.mi -g x.gbwt x.xg 2> /dev/null +t/46_vg_minimizer.t: line 26: 3288446 Illegal instruction vg minimizer --no-dist -t 1 -o x.mi -g x.gbwt x.xg +md5sum: x.mi: No such file or directory +t/46_vg_minimizer.t: line 31: 3288450 Illegal instruction vg minimizer --no-dist -t 1 -o x.mi -c -g x.gbwt x.xg +md5sum: x.mi: No such file or directory +t/46_vg_minimizer.t: line 36: 3288454 Illegal instruction vg minimizer --no-dist -t 1 -k 7 -w 3 -o x.mi -g x.gbwt x.xg +md5sum: x.mi: No such file or directory +t/46_vg_minimizer.t: line 41: 3288458 Illegal instruction vg gbwt -x x.xg -g x.gg x.gbwt +t/46_vg_minimizer.t: line 42: 3288459 Illegal instruction vg minimizer --no-dist -t 1 -g x.gbwt -o x.mi x.gg +md5sum: x.mi: No such file or directory +t/46_vg_minimizer.t: line 47: 3288463 Illegal instruction vg gbwt -x x.xg -g x.gbz --gbz-format x.gbwt +t/46_vg_minimizer.t: line 48: 3288464 Illegal instruction vg minimizer --no-dist -t 1 -o x.mi x.gbz +md5sum: x.mi: No such file or directory +t/46_vg_minimizer.t: line 53: 3288468 Illegal instruction vg minimizer -t 1 -o x.mi -g x.gbwt -d x.dist x.gg +t/46_vg_minimizer.t: line 62: 3288470 Illegal instruction vg construct -r small/xy.fa -v small/xy2.vcf.gz -R x -C -a > x.vg 2> /dev/null +t/46_vg_minimizer.t: line 63: 3288471 Illegal instruction vg construct -r small/xy.fa -v small/xy2.vcf.gz -R y -C -a > y.vg 2> /dev/null +t/46_vg_minimizer.t: line 64: 3288472 Illegal instruction vg ids -j x.vg y.vg +t/46_vg_minimizer.t: line 65: 3288473 Illegal instruction vg index -x x.xg -G x.gbwt -v small/xy2.vcf.gz x.vg +t/46_vg_minimizer.t: line 66: 3288474 Illegal instruction vg index -x y.xg -G y.gbwt -v small/xy2.vcf.gz y.vg +t/46_vg_minimizer.t: line 69: 3288475 Illegal instruction vg minimizer --no-dist -t 1 -o x.mi -g x.gbwt x.xg +t/46_vg_minimizer.t: line 71: 3288476 Illegal instruction vg minimizer --no-dist -t 1 -l x.mi -o xy.mi -g y.gbwt y.xg +md5sum: xy.mi: No such file or directory t/46_vg_minimizer.t ... 1..16 -ok 1 - default parameters -ok 2 - distance index or --no-dist is required -ok 3 - single-threaded construction -ok 4 - construction is deterministic -ok 5 - syncmer index -ok 6 - construction is deterministic -ok 7 - minimizer parameters -ok 8 - setting -k -w works correctly -ok 9 - construction from GBWTGraph -ok 10 - construction is deterministic -ok 11 - construction from GBZ -ok 12 - construction is deterministic -ok 13 - construction with payload -ok 14 - multiple graphs: first -ok 15 - multiple graphs: second -ok 16 - construction is deterministic -ok - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. +not ok 1 - default parameters +# got: '132' +# expected: '0' +not ok 2 - distance index or --no-dist is required +# got: '132' +# expected: '1' +not ok 3 - single-threaded construction +# got: '132' +# expected: '0' +not ok 4 - unnamed test +# got: '0d75343d78d1e7d9e9fbc3d7d2386ce2' +# expected: 'construction is deterministic' +not ok 5 - syncmer index +# got: '132' +# expected: '0' +not ok 6 - unnamed test +# got: '74d836b46799590835c7d61e283df4f0' +# expected: 'construction is deterministic' +not ok 7 - minimizer parameters +# got: '132' +# expected: '0' +not ok 8 - unnamed test +# got: '7260e5ea22f063a8dff1f9dd60f92288' +# expected: 'setting -k -w works correctly' +not ok 9 - construction from GBWTGraph +# got: '132' +# expected: '0' +not ok 10 - unnamed test +# got: '0d75343d78d1e7d9e9fbc3d7d2386ce2' +# expected: 'construction is deterministic' +not ok 11 - construction from GBZ +# got: '132' +# expected: '0' +not ok 12 - unnamed test +# got: '0d75343d78d1e7d9e9fbc3d7d2386ce2' +# expected: 'construction is deterministic' +not ok 13 - construction with payload +# got: '132' +# expected: '0' +not ok 14 - multiple graphs: first +# got: '132' +# expected: '0' +not ok 15 - multiple graphs: second +# got: '132' +# expected: '0' +not ok 16 - unnamed test +# got: '1ca39921b15cc3e7d27919a3ec7f47fa' +# expected: 'construction is deterministic' +Failed 16/16 subtests +t/47_vg_dotplot.t: line 10: 3288485 Illegal instruction vg msga -f GRCh38_alts/FASTA/HLA/V-352962.fa -t 1 -k 16 > hla.vg +t/47_vg_dotplot.t: line 11: 3288486 Illegal instruction vg index -x hla.xg hla.vg +t/47_vg_dotplot.t: line 12: 3288487 Illegal instruction vg dotplot -x hla.xg > /dev/null t/47_vg_dotplot.t ..... 1..1 -ok 1 - vg dotplot runs successfully -ok -[vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. -[vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. -[vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. -[vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. -[vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. -warning [vg convert]: currently cannot convert GFA directly to XG; converting through another format -[vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. -[vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. -warning:[GFAParser] Skipping GFA P line: GFA format error: On pass 1: On line 27: Duplicate path GRCh38.chr1 exists in graph -index file ref.fa.fai not found, generating... -warning: Thread 2 encountered sequence of length 275, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -alignment: valid -graph: valid -warning: Thread 34 encountered sequence of length 275, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -alignment: valid -graph: valid +not ok 1 - vg dotplot runs successfully +# got: '132' +# expected: '0' +Failed 1/1 subtests +t/48_vg_convert.t: line 12: 3288490 Illegal instruction vg construct -r complex/c.fa -v complex/c.vcf.gz > c.vg +t/48_vg_convert.t: line 15: 3288502 Illegal instruction vg convert c.vg -x > c.xg +t/48_vg_convert.t: line 16: 3288503 Illegal instruction vg convert c.xg -v > c1.vg +t/48_vg_convert.t: line 23: 3288517 Illegal instruction vg convert c.vg -a > c.hg +t/48_vg_convert.t: line 24: 3288518 Illegal instruction vg convert c.hg -v > c1.vg +t/48_vg_convert.t: line 31: 3288532 Illegal instruction vg convert c.vg -p > c.pg +t/48_vg_convert.t: line 32: 3288533 Illegal instruction vg convert c.pg -v > c1.vg +t/48_vg_convert.t: line 39: 3288547 Illegal instruction vg convert c.vg -f > c.gfa +t/48_vg_convert.t: line 40: 3288548 Illegal instruction vg convert -g c.gfa -v > c1.vg +t/48_vg_convert.t: line 48: 3288562 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > x.vg +t/48_vg_convert.t: line 49: 3288563 Illegal instruction vg view x.vg > x.gfa +t/48_vg_convert.t: line 65: 3288626 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > x.vg +t/48_vg_convert.t: line 66: 3288627 Illegal instruction vg index x.vg -g x.gcsa +t/48_vg_convert.t: line 67: 3288628 Illegal instruction vg sim -x x.vg -n 10 -s 23 -a > sim.gam +t/48_vg_convert.t: line 68: 3288629 Illegal instruction vg map -x x.vg -g x.gcsa -G sim.gam > sim-rm.gam +t/48_vg_convert.t: line 69: 3288630 Illegal instruction vg convert x.vg -G sim-rm.gam -t 1 > sim-rm.gaf +t/48_vg_convert.t: line 70: 3288631 Illegal instruction vg convert x.vg -F sim-rm.gaf -t 1 + 3288632 | vg convert x.vg -G - -t 1 > sim-rm2.gaf +t/48_vg_convert.t: line 84: 3288646 Illegal instruction vg map -s "TAATGGATATGTTAAGCTTTTTTTTTCTTTGATTTATTTGAAAAGACGTTTGACAATCTATCGGGTAATGTGGGGAAA" -x x.vg -g x.gcsa > mut.gam +t/48_vg_convert.t: line 86: 3288647 Illegal instruction vg map -s "TTTCCCCACATTACCCGATAGATTGTCAAACGTCTTTTCAAATAAATCAAAGAAAAAAAAAGCTTAACATATCCATTA" -x x.vg -g x.gcsa >> mut.gam +t/48_vg_convert.t: line 88: 3288648 Illegal instruction vg convert x.vg -G mut.gam -t 1 > mut.gaf +t/48_vg_convert.t: line 89: 3288649 Illegal instruction vg convert x.vg -F mut.gaf -t 1 > mut-back.gam +t/48_vg_convert.t: line 100: 3288660 Illegal instruction vg convert x.vg -G mut-back.gam -t 1 > mut-back.gaf +t/48_vg_convert.t: line 111: 3288662 Illegal instruction vg convert x.vg -F mut.cg.gaf -t 1 + 3288663 | vg convert x.vg -G - -t 1 > mut.cs.back.gaf +t/48_vg_convert.t: line 118: 3288667 Illegal instruction vg construct -r 1mb1kgp/z.fa -v 1mb1kgp/z.vcf.gz > z.vg 2> /dev/null +t/48_vg_convert.t: line 119: 3288668 Illegal instruction vg sim -n 10000 -s 23 -a -x z.vg > sim.gam +t/48_vg_convert.t: line 120: 3288669 Illegal instruction vg construct -r 1mb1kgp/z.fa > zflat.vg +t/48_vg_convert.t: line 121: 3288670 Illegal instruction vg index zflat.vg -g zflat.gcsa +t/48_vg_convert.t: line 122: 3288671 Illegal instruction vg map -x zflat.vg -g zflat.gcsa -G sim.gam > sim-map.gam +t/48_vg_convert.t: line 124: 3288674 Illegal instruction vg convert zflat.vg -F sim-map.gaf.gz > sim-map-back.gam +t/48_vg_convert.t: line 135: 3288687 Done printf '{"name": "split", "path": {"mapping": [{"edit": [{"from_length": 13, "to_length": 13}], "position": {"node_id": "1", "offset": "10"}}, {"edit": [{"from_length": 2, "to_length": 2}], "position": {"node_id": "3", "offset": "5"}}]}}' + 3288688 Illegal instruction | vg view -JaG - > split.gam +t/48_vg_convert.t: line 136: 3288689 Illegal instruction vg convert zflat.vg -G split.gam > split.gaf +t/48_vg_convert.t: line 138: 3288691 Illegal instruction vg convert zflat.vg -F split.gaf + 3288692 | vg convert zflat.vg -G - > split-back.gaf +t/48_vg_convert.t: line 156: 3288695 Done printf "H\tVN:Z:1.0 +S\t73333\tGGTGGGCGAGGACCTCCACACGTGTCACCA +S\t73368\tGCCCCT +S\t72943\tGGCGACTCTTCAGCAAGCCCCTCCACACGTGT +S\t72940\tC +S\t72941\tGGCCAGGT +S\t73255\tACTCTTCAGCAGGCCCCTCTGGT +S\t72942\tGGGCGAGGACCTCCACACGTGTCACCAGGCCA +S\t73318\tTCAGCA +S\t73367\tA +S\t73271\tA +S\t73289\tC +S\t73317\tC\n" + 3288696 Illegal instruction | vg convert -g - -p > soft.pg +t/48_vg_convert.t: line 157: 3288697 Done printf '{"annotation": {"fragment_length": 242, "fragment_length_distribution": "-I 561.110526 -D 141.152986", "mapq_applied_cap": 23.832780374978935, "mapq_extended_cap": 15, "mapq_uncapped": 10.325140756048304, "secondary_scores": [187.15265582416521, 182.4063994408188]}, "identity": 0.89682539682539686, "mapping_quality": 10, "name": "ERR903030.2067", "path": {"mapping": [{"edit": [{"from_length": 6, "to_length": 6}], "position": {"is_reverse": true, "node_id": "72943", "offset": "26"}}, {"edit": [{"from_length": 32, "to_length": 32}], "position": {"is_reverse": true, "node_id": "72942"}, "rank": "1"}, {"edit": [{"from_length": 23, "to_length": 23}], "position": {"is_reverse": true, "node_id": "73255"}, "rank": "2"}, {"edit": [{"from_length": 1, "to_length": 1}], "position": {"is_reverse": true, "node_id": "73271"}, "rank": "3"}, {"edit": [{"from_length": 8, "to_length": 8}], "position": {"is_reverse": true, "node_id": "72941"}, "rank": "4"}, {"edit": [{"from_length": 7, "to_length": 7}, {"from_length": 1, "sequence": "C", "to_length": 1}, {"from_length": 2, "to_length": 2}, {"from_length": 1, "sequence": "G", "to_length": 1}, {"from_length": 19, "to_length": 19}], "position": {"is_reverse": true, "node_id": "73333"}, "rank": "5"}, {"edit": [{"from_length": 1, "to_length": 1}], "position": {"is_reverse": true, "node_id": "72940"}, "rank": "6"}, {"edit": [{"from_length": 1, "to_length": 1}], "position": {"is_reverse": true, "node_id": "73289"}, "rank": "7"}, {"edit": [{"from_length": 6, "to_length": 6}], "position": {"is_reverse": true, "node_id": "73368"}, "rank": "8"}, {"edit": [{"from_length": 1, "sequence": "G", "to_length": 1}], "position": {"is_reverse": true, "node_id": "73367"}, "rank": "9"}, {"edit": [{"from_length": 6, "to_length": 6}], "position": {"is_reverse": true, "node_id": "73318"}, "rank": "10"}, {"edit": [{"from_length": 1, "to_length": 1}], "position": {"is_reverse": true, "node_id": "73317"}, "rank": "11"}, {"edit": [{"sequence": "GGGTGGCCTG", "to_length": 10}], "position": {"is_reverse": true, "node_id": "73317", "offset": "1"}, "rank": "12"}]}, "quality": "ISEhISEmJiUmJCYmJSYlJiYmJiYmJCYjJiYdIRsmIyUmJiYmJiElJg4PDx0PDyEkIhsYJCYiECQQJBAcGR0kHx0QGSQPJCImHSElHR0PJA4OGyQbIxwPIg0iHw8PGRwiIR0jAgICAgICAgICAgICAgICAgICAgICAgICAgIC", "sample_name": "HG00514_961a37c_gssw", "score": 106, "sequence": "GTCGCCTGGCCTGGTGACACGTGTGGAGGTCCTCGCCCACCAGAGGGGCCTGCTGAAGAGTTACCTGGCCTGGTGACCCGGGTGGAGGTCCTCGCCCACCGGAGGGGCGTGCTGAGGGGTGGCCTG"}' + 3288698 Illegal instruction | vg view -JaG - > soft.gam +t/48_vg_convert.t: line 158: 3288699 Illegal instruction vg convert soft.pg -G soft.gam > soft.gaf +t/48_vg_convert.t: line 164: 3288706 Illegal instruction vg convert soft.pg -F soft.gaf + 3288707 | vg convert soft.pg -G - > soft2.gaf +t/48_vg_convert.t: line 171: 3288710 Done printf "H\tVN:Z:1.0 +S\t91194329\tAGGAAGGAGAGGGAG\n" + 3288711 Illegal instruction | vg convert -g - -p > floating-ins.pg +t/48_vg_convert.t: line 172: 3288712 Done printf '{"annotation": {"fragment_length": 1098, "fragment_length_distribution": "-I 542.973684 -D 141.206118", "mapq_applied_cap": 46.364361584299516, "mapq_extended_cap": "Infinity", "mapq_uncapped": 1.5051499783199018, "rescued": true, "secondary_scores": [99.415737573445895]}, "mapping_quality": 1, "name": "ERR903030.51990324", "path": {"mapping": [{"edit": [{"sequence": "GGGCACGGTGGCTCACAGCTGTCACCACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN", "to_length": 126}], "position": {"is_reverse": true, "node_id": "91194329", "offset": "15"}, "rank": "1"}]}, "quality": "ISEhICEhJCIkJiYdJiUQJSYmHyMmIxAkJiICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgIC", "sample_name": "HG00514_961a37c", "sequence": "GGGCACGGTGGCTCACAGCTGTCACCACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"}' + 3288713 Illegal instruction | vg view -JaG - > floating-ins.gam +t/48_vg_convert.t: line 173: 3288714 Illegal instruction vg convert floating-ins.pg -G floating-ins.gam > floating-ins.gaf +t/48_vg_convert.t: line 179: 3288721 Illegal instruction vg convert floating-ins.pg -F floating-ins.gaf + 3288722 | vg convert floating-ins.pg -G - > floating-ins2.gaf +t/48_vg_convert.t: line 194: 3288738 Illegal instruction vg convert -g tiny/tiny.rgfa -T gfa-id-mapping.tsv > /dev/null +awk: fatal: cannot open file `gfa-id-mapping.tsv' for reading: No such file or directory +awk: fatal: cannot open file `gfa-id-mapping.tsv' for reading: No such file or directory +t/48_vg_convert.t: line 206: 3288752 Illegal instruction vg convert -g tiny/tiny.gfa -v + 3288753 | vg convert - -f -P x > tiny.gfa.rgfa +t/48_vg_convert.t: line 220: 3288764 Illegal instruction vg gbwt -o components.gbwt -g components.gg -G graphs/components_walks.gfa +t/48_vg_convert.t: line 222: 3288766 Illegal instruction vg convert -b components.gbwt -a components.gg > components.hg 2> /dev/null +cmp: EOF on converted.gfa which is empty +cmp: EOF on converted.gfa which is empty +t/48_vg_convert.t: line 234: 3288779 Illegal instruction vg gbwt -g components.gbz --gbz-format -G graphs/components_walks.gfa +t/48_vg_convert.t: line 235: 3288780 Illegal instruction vg convert -a components.gbz > components.hg 2> /dev/null +cmp: EOF on converted.gfa which is empty +t/48_vg_convert.t: line 243: 3288787 Illegal instruction vg convert -b components.gbwt -f -t 1 components.gg > extracted.gfa +cmp: EOF on extracted.gfa which is empty +cmp: EOF on extracted.gfa which is empty +t/48_vg_convert.t: line 253: 3288792 Illegal instruction vg convert -f -t 1 components.gbz > extracted.gfa +cmp: EOF on extracted.gfa which is empty +t/48_vg_convert.t: line 263: 3288794 Illegal instruction vg convert -g graphs/components_paths_walks.gfa -a > components.hg +cmp: EOF on converted.gfa which is empty +t/48_vg_convert.t: line 276: 3288803 Illegal instruction vg gbwt -o components.gbwt -g components.gg -G graphs/components_paths_walks.gfa +t/48_vg_convert.t: line 277: 3288804 Illegal instruction vg gbwt -g components.gbz --gbz-format -G graphs/components_paths_walks.gfa +t/48_vg_convert.t: line 278: 3288805 Illegal instruction vg convert -g -a graphs/components_paths_walks.gfa > direct.hg +t/48_vg_convert.t: line 284: 3288811 Illegal instruction vg convert -b components.gbwt -a components.gg > components.hg +t/48_vg_convert.t: line 294: 3288818 Illegal instruction vg convert -a components.gbz > components.hg +t/48_vg_convert.t: line 304: 3288825 Illegal instruction vg convert -b components.gbwt -x components.gg > components.xg +t/48_vg_convert.t: line 314: 3288832 Illegal instruction vg convert -x components.gbz > components.xg +t/48_vg_convert.t: line 324: 3288839 Illegal instruction vg convert -x --drop-haplotypes components.gbz > no_haplotypes.xg +t/48_vg_convert.t: line 327: 3288843 Illegal instruction vg convert -xa --drop-haplotypes components.gbz > no_haplotypes.hg +t/48_vg_convert.t: line 332: 3288847 Illegal instruction vg convert -b components.gbwt -f -t 1 components.gg > extracted.gfa +cmp: EOF on extracted.gfa which is empty +cmp: EOF on extracted.gfa which is empty +t/48_vg_convert.t: line 342: 3288852 Illegal instruction vg convert -b components.gbwt -t 1 components.gg -a > extracted.hg +cmp: EOF on extracted.gfa which is empty +t/48_vg_convert.t: line 348: 3288856 Illegal instruction vg convert --no-wline -f -t1 extracted.hg > no-walks.gfa +t/48_vg_convert.t: line 354: 3288866 Illegal instruction vg convert --gbwtgraph-algorithm -f -t 1 components.gbz > gbz.gfa +cmp: EOF on gbz.gfa which is empty +cmp: EOF on sorted.gfa which is empty +t/48_vg_convert.t: line 365: 3288871 Illegal instruction vg gbwt --gbz-format -g chopping.gbz --max-node 2 -G graphs/chopping_walks.gfa +t/48_vg_convert.t: line 366: 3288872 Illegal instruction vg convert -f -t 1 chopping.gbz > with-translation.gfa +t/48_vg_convert.t: line 369: 3288874 Illegal instruction vg convert -f -t 1 --no-translation chopping.gbz > no-translation.gfa +t/48_vg_convert.t: line 388: 3288886 Illegal instruction vg gbwt -G graphs/gfa_with_reference.gfa --gbz-format -g gfa_with_reference.gbz +t/48_vg_convert.t: line 392: 3288890 Illegal instruction vg convert -f gfa_with_reference.gbz > extracted.gfa +t/48_vg_convert.t: line 396: 3288894 Illegal instruction vg convert -g graphs/gfa_with_reference.gfa -a > gfa_with_reference.hg +t/48_vg_convert.t: line 400: 3288898 Illegal instruction vg convert gfa_with_reference.hg -f > extracted.gfa +t/48_vg_convert.t: line 408: 3288904 Illegal instruction vg convert -a graphs/rgfa_with_reference.rgfa > rgfa_with_reference.hg +t/48_vg_convert.t: line 409: 3288905 Illegal instruction vg gbwt -x rgfa_with_reference.hg -E --gbz-format -g rgfa_with_reference.gbz +t/48_vg_convert.t: line 413: 3288909 Illegal instruction vg convert -f rgfa_with_reference.gbz > extracted.gfa +t/48_vg_convert.t: line 420: 3288913 Illegal instruction vg convert -a graphs/components_paths_rgfa.gfa > components_paths_rgfa.hg +t/48_vg_convert.t: line 425: 3288917 Illegal instruction vg convert -a graphs/gfa_two_part_reference.gfa > gfa_two_part_reference.hg +t/48_vg_convert.t: line 488: 3288994 Illegal instruction vg construct -r ref.fa > ref.vg +t/48_vg_convert.t: line 489: 3288995 Illegal instruction vg index -g ref.gcsa -k 16 ref.vg +t/48_vg_convert.t: line 490: 3288996 Illegal instruction vg map -f query.fa -x ref.vg -g ref.gcsa > out.gam +t/48_vg_convert.t: line 491: 3288997 Illegal instruction vg convert ref.vg -G out.gam > out.gaf +t/48_vg_convert.t: line 492: 3288998 Illegal instruction vg convert ref.vg -F out.gaf > out2.gam +t/48_vg_convert.t: line 493: 3288999 Illegal instruction vg convert ref.vg -G out2.gam > out2.gaf +t/48_vg_convert.t: line 496: 3289001 Illegal instruction vg validate ref.vg -a out2.gam +t/48_vg_convert.t: line 501: 3289003 Illegal instruction vg construct -r ref.fa -m 1000 > ref.vg +t/48_vg_convert.t: line 502: 3289004 Illegal instruction vg construct -r ref.fa > ref.vg +t/48_vg_convert.t: line 503: 3289005 Illegal instruction vg index -g ref.gcsa -k 16 ref.vg +t/48_vg_convert.t: line 504: 3289006 Illegal instruction vg map -f query.fa -x ref.vg -g ref.gcsa > out.gam +t/48_vg_convert.t: line 505: 3289007 Illegal instruction vg convert ref.vg -G out.gam > out.gaf +t/48_vg_convert.t: line 506: 3289008 Illegal instruction vg convert ref.vg -F out.gaf > out2.gam +t/48_vg_convert.t: line 507: 3289009 Illegal instruction vg convert ref.vg -G out2.gam > out2.gaf +t/48_vg_convert.t: line 510: 3289011 Illegal instruction vg validate ref.vg -a out2.gam t/48_vg_convert.t ..... 1..106 ok 1 - vg convert maintains same nodes throughout xg conversion @@ -22871,662 +29229,441 @@ ok 17 - vg convert gam -> gaf -> gam produces same gam Paths with snps and indels ok 18 - vg convert gam -> gaf -> gam preserves sequence ok 19 - vg convert gam -> gaf -> gam -> gaf makes same gaf twice in presence of indels and snps -ok 20 - vg convert cg-gaf -> gam -> cs-gaf gives expected output (snps converted to matches, insertion converted to Ns) +0a1 +> * 78 0 78 + >20>21>23>24>26>27>29>30>32>33>35 102 22 102 71 80 60 AS:i:47 cs:Z::13*GN*GN:8+NNN:16*GN*TN:18-ACTAG:16 +not ok 20 - vg convert cg-gaf -> gam -> cs-gaf gives expected output (snps converted to matches, insertion converted to Ns) +# got: '1' +# expected: '0' ok 21 - vg convert gam -> gaf -> gam preserves sequences of 1mb1kgp simulated reads ok 22 - vg convert gam -> gaf -> gam ->gaf makes same gaf each time on 1mb1kgp simulated reads -ok 23 - split alignment converted using deletions to represent internal offsets +not ok 23 - split alignment converted using deletions to represent internal offsets +# got: '' +# expected: 'cs:Z::13-CCAGTGCTCGCATC:2' ok 24 - vg convert gam -> gaf ->gam -> gaf makes same gaf each time for split alignment ok 25 - convert gam->gaf->gam on softclipped read preserves sequence ok 26 - convert gam->gaf->gam->gaf makes same gaf each time of soft clipped alignment ok 27 - convert gam->gaf->gam on read with floating insertion preserves sequence ok 28 - convert gam->gaf->gam->gaf makes same gaf each time of floating insertion alignment ok 29 - converting gfa and equivalent rgfa produces same output -ok 30 - rank-1 rgfa subpath found -ok 31 - 2nd column of gfa id translation file contains all rgfa nodes -ok 32 - 3rd column of gfa id translation file contains all gfa nodes +not ok 30 - rank-1 rgfa subpath found +# got: '' +# expected: 'y[35]' +1,15d0 +< 12 +< s1 +< s10 +< s11 +< s13 +< s14 +< s15 +< s2 +< s3 +< s4 +< s5 +< s6 +< s7 +< s8 +< s9 +not ok 31 - 2nd column of gfa id translation file contains all rgfa nodes +# got: '1' +# expected: '0' +1,15d0 +< 1 +< 10 +< 11 +< 12 +< 13 +< 14 +< 15 +< 2 +< 3 +< 4 +< 5 +< 6 +< 7 +< 8 +< 9 +not ok 32 - 3rd column of gfa id translation file contains all gfa nodes +# got: '1' +# expected: '0' ok 33 - rgfa output wrote no P-lines ok 34 - rgfa export roundtrips back to normal P-lines -ok 35 - GBWTGraph to HashGraph conversion -ok 36 - GFA -> GBWTGraph -> HashGraph -> GFA conversion maintains segments -ok 37 - GFA -> GBWTGraph -> HashGraph -> GFA conversion maintains walks -ok 38 - GBZ to HashGraph conversion -ok 39 - GFA -> GBZ -> HashGraph -> GFA conversion maintains segments -ok 40 - GBWTGraph to GFA conversion with walks, GBWTGraph algorithm -ok 41 - GBWTGraph to GFA conversion with GBWTGraph algorithm creates the correct normalized GFA file +not ok 35 - GBWTGraph to HashGraph conversion +# got: '132' +# expected: '0' +not ok 36 - GFA -> GBWTGraph -> HashGraph -> GFA conversion maintains segments +# got: '1' +# expected: '0' +not ok 37 - GFA -> GBWTGraph -> HashGraph -> GFA conversion maintains walks +# got: '1' +# expected: '0' +not ok 38 - GBZ to HashGraph conversion +# got: '132' +# expected: '0' +not ok 39 - GFA -> GBZ -> HashGraph -> GFA conversion maintains segments +# got: '1' +# expected: '0' +not ok 40 - GBWTGraph to GFA conversion with walks, GBWTGraph algorithm +# got: '132' +# expected: '0' +not ok 41 - GBWTGraph to GFA conversion with GBWTGraph algorithm creates the correct normalized GFA file +# got: '1' +# expected: '0' ok 42 - GBWTGraph to GFA conversion with walks, vg algorithm -ok 43 - GBWTGraph to GFA conversion with vg algorithm creates the correct possibly-unnormalized GFA file -ok 44 - GBZ to GFA conversion with walks, GBWTGraph algorithm -ok 45 - GBZ to GFA conversion with GBWTGraph algorithm creates the correct normalized GFA file -ok 46 - GFA to HashGraph conversion -ok 47 - GFA -> HashGraph -> GFA conversion maintains segments, links, walks, and paths -ok 48 - GBWTGraph to HashGraph conversion with generic paths +not ok 43 - GBWTGraph to GFA conversion with vg algorithm creates the correct possibly-unnormalized GFA file +# got: '1' +# expected: '0' +not ok 44 - GBZ to GFA conversion with walks, GBWTGraph algorithm +# got: '132' +# expected: '0' +not ok 45 - GBZ to GFA conversion with GBWTGraph algorithm creates the correct normalized GFA file +# got: '1' +# expected: '0' +not ok 46 - GFA to HashGraph conversion +# got: '132' +# expected: '0' +not ok 47 - GFA -> HashGraph -> GFA conversion maintains segments, links, walks, and paths +# got: '1' +# expected: '0' +not ok 48 - GBWTGraph to HashGraph conversion with generic paths +# got: '132' +# expected: '0' ok 49 - GBWTGraph to HashGraph conversion creates the correct generic paths ok 50 - GBWTGraph to HashGraph conversion creates the correct haplotype paths -ok 51 - GBZ to HashGraph conversion with generic paths +not ok 51 - GBZ to HashGraph conversion with generic paths +# got: '132' +# expected: '0' ok 52 - GBZ to HashGraph conversion creates the correct generic paths ok 53 - GBZ to HashGraph conversion creates the correct haplotype paths -ok 54 - GBWTGraph to XG conversion with generic paths +not ok 54 - GBWTGraph to XG conversion with generic paths +# got: '132' +# expected: '0' ok 55 - GBWTGraph to XG conversion creates the correct generic paths ok 56 - GBWTGraph to XG conversion creates the correct haplotype paths -ok 57 - GBZ to XG conversion with generic paths +not ok 57 - GBZ to XG conversion with generic paths +# got: '132' +# expected: '0' ok 58 - GBZ to XG conversion creates the correct generic paths ok 59 - GBZ to XG conversion creates the correct haplotype paths -ok 60 - GBZ to XG conversion while dropping haplotypes -ok 61 - No haplotypes in the converted graph -ok 62 - GBZ to HashGraph conversion while dropping haplotypes -ok 63 - No haplotypes in the converted graph -ok 64 - GBWTGraph to GFA conversion with paths and walks, GBWTGraph algorithm -ok 65 - GBWTGraph to GFA conversion with GBWTGraph algorithm creates the expected normalized GFA file +not ok 60 - GBZ to XG conversion while dropping haplotypes +# got: '132' +# expected: '0' +not ok 61 - No haplotypes in the converted graph +# got: '0' +# expected: '2' +not ok 62 - GBZ to HashGraph conversion while dropping haplotypes +# got: '132' +# expected: '0' +not ok 63 - No haplotypes in the converted graph +# got: '0' +# expected: '2' +not ok 64 - GBWTGraph to GFA conversion with paths and walks, GBWTGraph algorithm +# got: '132' +# expected: '0' +not ok 65 - GBWTGraph to GFA conversion with GBWTGraph algorithm creates the expected normalized GFA file +# got: '1' +# expected: '0' ok 66 - GBWTGraph to GFA conversion with paths and walks, vg algorithm -ok 67 - GBWTGraph to GFA conversion with vg algorithm creates the correct possibly-unnormalized GFA file -ok 68 - GBWTGraph to HashGraph conversion with paths and walks +not ok 67 - GBWTGraph to GFA conversion with vg algorithm creates the correct possibly-unnormalized GFA file +# got: '1' +# expected: '0' +not ok 68 - GBWTGraph to HashGraph conversion with paths and walks +# got: '132' +# expected: '0' ok 69 - HashGraph to GFA conversion with paths and walks -ok 70 - GBWTGraph to HashGraph to GFA conversion creates the correct possibly-unnormalized GFA file -ok 71 - HashGraph to GFA conversion writing walks as paths +not ok 70 - GBWTGraph to HashGraph to GFA conversion creates the correct possibly-unnormalized GFA file +# got: '1' +# expected: '0' +not ok 71 - HashGraph to GFA conversion writing walks as paths +# got: '132' +# expected: '0' ok 72 - HashGraph to GFA conversion writing walks as paths produces no walks -ok 73 - HashGraph to GFA conversion writing walks as paths produces all expected paths -ok 74 - GBZ to GFA conversion with paths and walks, GBWTGraph algorithm -ok 75 - GBZ to GFA conversion with GBWTGraph algorithm creates the correct normalized GFA file -ok 76 - GBZ to GFA conversion works with multiple threads -ok 77 - GBZ to GFA with translation -ok 78 - 8 segments -ok 79 - GBZ to GFA without translation -ok 80 - 9 segments +not ok 73 - HashGraph to GFA conversion writing walks as paths produces all expected paths +# got: '0' +# expected: '6' +not ok 74 - GBZ to GFA conversion with paths and walks, GBWTGraph algorithm +# got: '132' +# expected: '0' +not ok 75 - GBZ to GFA conversion with GBWTGraph algorithm creates the correct normalized GFA file +# got: '1' +# expected: '0' +not ok 76 - GBZ to GFA conversion works with multiple threads +# got: '1' +# expected: '0' +not ok 77 - GBZ to GFA with translation +# got: '132' +# expected: '0' +not ok 78 - 8 segments +# got: '0' +# expected: '8' +not ok 79 - GBZ to GFA without translation +# got: '132' +# expected: '0' +not ok 80 - 9 segments +# got: '0' +# expected: '9' ok 81 - GFA -> GBZ conversion preserves path metadata ok 82 - GFA -> GBZ -> GFA conversion preserves path metadata ok 83 - GFA -> HashGraph conversion preserves path metadata ok 84 - GFA -> HashGraph -> GFA conversion preserves path metadata ok 85 - rGFA -> HashGraph -> GBZ conversion preserves path metadata ok 86 - rGFA -> HashGraph -> GBZ -> GFA conversion preserves path metadata -ok 87 - GFA -> HashGraph conversion works with redundant paths -ok 88 - GFA -> HashGraph conversion with redundant paths keeps one copy of the redundant path -ok 89 - GFA -> HashGraph conversion works with two-part reference path names -ok 90 - GFA -> HashGraph conversion with with two-part reference path names gets the right paths +not ok 87 - GFA -> HashGraph conversion works with redundant paths +# got: '132' +# expected: '0' +not ok 88 - GFA -> HashGraph conversion with redundant paths keeps one copy of the redundant path +# got: '0' +# expected: '1' +not ok 89 - GFA -> HashGraph conversion works with two-part reference path names +# got: '132' +# expected: '0' +not ok 90 - GFA -> HashGraph conversion with with two-part reference path names gets the right paths +# got: '0' +# expected: '2' ok 91 - No difference roundtripping a GFA if it's loaded as a GFA or HandleGraph -warning:[GFAParser] Streaming GFA file references node 6 before it is defined. GFA lines will be buffered in a temporary file. ok 92 - Streaming an unsorted GFA gives same output as sorted -ok 93 - Warning given when falling back to temp GFA buffer file +not ok 93 - Warning given when falling back to temp GFA buffer file +# got: '0' +# expected: '1' ok 94 - Streaming an sorted GFA gives same output as reading from file ok 95 - No warnings given when streamed GFA is sorted ok 96 - Modding GFA directly produces same output as going through convert ok 97 - Modding sorted GFA stream produces same output as going through convert -warning:[GFAParser] Streaming GFA file references node 6 before it is defined. GFA lines will be buffered in a temporary file. ok 98 - Modding unsorted GFA stream produces same output as going through convert -ok 99 - Warning given when falling back to temp GFA buffer file in mod +not ok 99 - Warning given when falling back to temp GFA buffer file in mod +# got: '0' +# expected: '1' ok 100 - Modding unsorted GFA file produces same output as going through convert ok 101 - No warnings given when input GFA file is unsorted ok 102 - rGFA handled consistently when streaming as when loaded from file ok 103 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output (GAF check) -ok 104 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output (GAM check) +not ok 104 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output (GAM check) +# got: '132' +# expected: '0' ok 105 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output for long node (GAF check) -ok 106 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output for long node (GAM check) -ok -[vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. +not ok 106 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output for long node (GAM check) +# got: '132' +# expected: '0' +Failed 47/106 subtests +t/49_vg_depth.t: line 10: 3289014 Illegal instruction vg construct -m 10 -r tiny/tiny.fa > flat.vg +t/49_vg_depth.t: line 11: 3289015 Illegal instruction vg view flat.vg + 3289016 Done | sed 's/CAAATAAGGCTTGGAAATTTTCTGGAGTTCTATTATATTCCAACTCTCTG/CAAATAAGGCTTGGAAATTTTCTGGAGATCTATTATACTCCAACTCTCTG/' + 3289017 | vg view -Fv - > 2snp.vg +t/49_vg_depth.t: line 12: 3289018 Illegal instruction vg sim -l 30 -x 2snp.vg -n 30 -a -s 1 > 2snp.sim +t/49_vg_depth.t: line 13: 3289019 Illegal instruction vg index -x flat.xg -g flat.gcsa -k 16 flat.vg +t/49_vg_depth.t: line 14: 3289020 Illegal instruction vg map -g flat.gcsa -x flat.xg -G 2snp.sim -k 8 > 2snp.gam +t/49_vg_depth.t: line 15: 3289021 Illegal instruction vg pack -x flat.xg -o 2snp.gam.cx -g 2snp.gam +t/49_vg_depth.t: line 22: 3289036 Illegal instruction vg augment flat.vg 2snp.gam -i > flat-aug.vg t/49_vg_depth.t ....... 1..6 -ok 1 - vg depth gets correct depth from gam -ok 2 - vg depth gets correct depth from pack -ok 3 - vg depth gets correct number of bins -ok 4 - vg depth gets correct depth from gaf +not ok 1 - unnamed test +# got: '18' +# expected: 'vg depth gets correct depth from gam' +not ok 2 - unnamed test +# got: '18' +# expected: 'vg depth gets correct depth from pack' +not ok 3 - vg depth gets correct number of bins +# got: '0' +# expected: '5' +not ok 4 - unnamed test +# got: '18' +# expected: 'vg depth gets correct depth from gaf' ok 5 - vg depth of paths reports all paths -ok 6 - vg depth of paths reports just path with selected prefix -ok -[IndexRegistry]: Constructing GBZ. -Guessing that x.gbwt is Giraffe GBWT -Guessing that x.xg is XG -Guessing that x.xg is XG -[IndexRegistry]: Combining Giraffe GBWT and GBWTGraph into GBZ. -Guessing that x.gbwt is Giraffe GBWT -Guessing that x.xg is XG -Guessing that x.gg is GBWTGraph -[IndexRegistry]: Constructing minimizer index. -Guessing that x.dist is Giraffe Distance Index -Guessing that x.gbwt is Giraffe GBWT -Guessing that x.min is Minimizers -Guessing that x.xg is XG -Guessing that x.gg is GBWTGraph -Guessing that x.dist is Giraffe Distance Index -Guessing that x.gbwt is Giraffe GBWT -Guessing that x.min is Minimizers -Guessing that x.xg is XG -Guessing that x.gg is GBWTGraph -Guessing that x.dist is Giraffe Distance Index -Guessing that x.gbwt is Giraffe GBWT -Guessing that x.min is Minimizers -Guessing that x.xg is XG -Guessing that x.gg is GBWTGraph -Guessing that x.dist is Giraffe Distance Index -Guessing that x.gbwt is Giraffe GBWT -Guessing that x.min is Minimizers -Guessing that x.xg is XG -Guessing that x.gg is GBWTGraph -[vg minimizer] warning: --bounded-syncmers is deprecated, use --closed-syncmers instead -Guessing that x.gg is GBWTGraph -Guessing that x.giraffe.gbz is Giraffe GBZ -Guessing that x.gg is GBWTGraph -Guessing that x.giraffe.gbz is Giraffe GBZ -Guessing that x.gg is GBWTGraph -Guessing that x.giraffe.gbz is Giraffe GBZ -[IndexRegistry]: Checking for phasing in VCF(s). -[IndexRegistry]: Chunking inputs for parallelism. -index file x.fa.fai not found, generating... -[IndexRegistry]: Constructing VG graph from FASTA and VCF input. -[IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. -[IndexRegistry]: Stripping allele paths from VG. -[IndexRegistry]: Constructing XG graph from VG graph. -[IndexRegistry]: Downsampling full GBWT. -[IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. -[IndexRegistry]: Constructing GBZ. -[IndexRegistry]: Constructing distance index for Giraffe. -[IndexRegistry]: Constructing minimizer index. -[IndexRegistry]: Checking for phasing in VCF(s). -Guessing that x.dist is Giraffe Distance Index -Guessing that x.min is Minimizers -Guessing that x.giraffe.gbz is Giraffe GBZ -[IndexRegistry]: Checking for phasing in VCF(s). -Guessing that x.dist is Giraffe Distance Index -Guessing that x.min is Minimizers -Guessing that x.giraffe.gbz is Giraffe GBZ -[IndexRegistry]: Checking for phasing in VCF(s). -Guessing that x.dist is Giraffe Distance Index -Guessing that x.min is Minimizers -Guessing that x.giraffe.gbz is Giraffe GBZ -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -warning[vg::giraffe]: Finalizing fragment length distribution before reaching maximum sample size - mapped 1 reads single ended with 0 pairs of reads left unmapped - mean: 0, stdev: 1 -[IndexRegistry]: Checking for phasing in VCF(s). -Guessing that x.dist is Giraffe Distance Index -Guessing that x.min is Minimizers -Guessing that x.giraffe.gbz is Giraffe GBZ -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -[IndexRegistry]: Checking for phasing in VCF(s). -[IndexRegistry]: Chunking inputs for parallelism. -index file xy.fa.fai not found, generating... -[IndexRegistry]: Chunking FASTA(s). -[IndexRegistry]: Chunking VCF(s). -[IndexRegistry]: Constructing VG graph from FASTA and VCF input. -[IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. -[IndexRegistry]: Merging contig GBWTs. -[IndexRegistry]: Stripping allele paths from VG. -[IndexRegistry]: Constructing XG graph from VG graph. -[IndexRegistry]: Downsampling full GBWT. -[IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. -[IndexRegistry]: Constructing GBZ. -[IndexRegistry]: Constructing distance index for Giraffe. -[IndexRegistry]: Constructing minimizer index. -[IndexRegistry]: Checking for phasing in VCF(s). -Guessing that xy.dist is Giraffe Distance Index -Guessing that xy.min is Minimizers -Guessing that xy.giraffe.gbz is Giraffe GBZ -[IndexRegistry]: Checking for phasing in VCF(s). -Guessing that xy.dist is Giraffe Distance Index -Guessing that xy.min is Minimizers -Guessing that xy.giraffe.gbz is Giraffe GBZ -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -[IndexRegistry]: Checking for phasing in VCF(s). -Guessing that xy.dist is Giraffe Distance Index -Guessing that xy.min is Minimizers -Guessing that xy.giraffe.gbz is Giraffe GBZ -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -[IndexRegistry]: Checking for phasing in VCF(s). -Guessing that xy.dist is Giraffe Distance Index -Guessing that xy.min is Minimizers -Guessing that xy.giraffe.gbz is Giraffe GBZ -[IndexRegistry]: Checking for phasing in VCF(s). -Guessing that xy.dist is Giraffe Distance Index -Guessing that xy.min is Minimizers -Guessing that xy.giraffe.gbz is Giraffe GBZ -[IndexRegistry]: Checking for phasing in VCF(s). -Guessing that xy.dist is Giraffe Distance Index -Guessing that xy.min is Minimizers -Guessing that xy.giraffe.gbz is Giraffe GBZ -[IndexRegistry]: Checking for phasing in VCF(s). -Guessing that xy.dist is Giraffe Distance Index -Guessing that xy.min is Minimizers -Guessing that xy.giraffe.gbz is Giraffe GBZ -[IndexRegistry]: Constructing distance index for Giraffe. -[IndexRegistry]: Constructing minimizer index. -warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. -[vg autoindex] Executing command: vg autoindex -p brca -w giraffe -g graphs/cactus-BRCA2.gfa -[IndexRegistry]: Checking for haplotype lines in GFA. -[IndexRegistry]: Constructing VG graph from GFA input. -[IndexRegistry]: Constructing XG graph from VG graph. -[IndexRegistry]: Constructing a greedy path cover GBWT -[IndexRegistry]: Constructing GBZ using NamedNodeBackTranslation. -[IndexRegistry]: Constructing distance index for Giraffe. -[IndexRegistry]: Constructing minimizer index. -[W::bgzf_read_block] EOF marker is absent. The input may be truncated -terminate called after throwing an instance of 'std::runtime_error' - what(): [vg::io::MessageIterator] obsolete, invalid, or corrupt input at message 79256662206 group 79256662202 -━━━━━━━━━━━━━━━━━━━━ -Crash report for vg v1.59.0 "Casatico" -Stack trace (most recent call last): -#24 Object "/usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2", at 0xffffffffffffffff, in -#23 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583f99a3380, in _start -#22 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fe432233e24, in __libc_start_main -#21 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fe432233d67, in -#20 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583fa1c298f, in vg::subcommand::Subcommand::operator()(int, char**) const - | Source "src/subcommand/subcommand.cpp", line 75, in operator() - Source "/usr/include/c++/14/bits/std_function.h", line 591, in operator() [0x5583fa1c298f] - 588: { - 589: if (_M_empty()) - 590: __throw_bad_function_call(); - > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); - 592: } - 593: - 594: #if __cpp_rtti -#19 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583fa12d443, in main_index(int, char**) - Source "src/subcommand/index_main.cpp", line 709, in main_index [0x5583fa12d443] -#18 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583fa131645, in std::tuple >, std::unique_ptr > > vg::io::VPKG::try_load_first(std::__cxx11::basic_string, std::allocator > const&) - Source "./include/vg/io/vpkg.hpp", line 112, in try_load_first [0x5583fa131645] -#17 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583fa1313ee, in std::tuple >, std::unique_ptr > > vg::io::VPKG::try_load_first(std::istream&, std::__cxx11::basic_string, std::allocator > const&) - Source "./include/vg/io/vpkg.hpp", line 64, in try_load_first [0x5583fa1313ee] -#16 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583f9fdcfde, in vg::io::VPKG::with_putback(std::istream&, std::function const&) - | Source "./include/vg/io/vpkg.hpp", line 595, in operator() - Source "/usr/include/c++/14/bits/std_function.h", line 591, in with_putback [0x5583f9fdcfde] - 588: { - 589: if (_M_empty()) - 590: __throw_bad_function_call(); - > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); - 592: } - 593: - 594: #if __cpp_rtti -#15 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583fa131a99, in std::_Function_handler(std::istream&, std::__cxx11::basic_string, std::allocator > const&)::{lambda(std::istream&)#1}>::_M_invoke(std::_Any_data const&, std::istream&) - | Source "/usr/include/c++/14/bits/std_function.h", line 290, in __invoke_r(std::istream&, const std::string&)::&, std::basic_istream >&> - | 288: _M_invoke(const _Any_data& __functor, _ArgTypes&&... __args) - | 289: { - | > 290: return std::__invoke_r<_Res>(*_Base::_M_get_pointer(__functor), - | 291: std::forward<_ArgTypes>(__args)...); - | 292: } - | Source "/usr/include/c++/14/bits/invoke.h", line 150, in __invoke_impl(std::istream&, const std::string&)::&, std::basic_istream >&> - | 148: using __type = typename __result::type; - | 149: using __tag = typename __result::__invoke_type; - | > 150: std::__invoke_impl<__type>(__tag{}, std::forward<_Callable>(__fn), - | 151: std::forward<_Args>(__args)...); - | 152: } - | Source "/usr/include/c++/14/bits/invoke.h", line 61, in operator() - | 59: constexpr _Res - | 60: __invoke_impl(__invoke_other, _Fn&& __f, _Args&&... __args) - | > 61: { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); } - | 62: - | 63: template - | Source "./include/vg/io/vpkg.hpp", line 77, in try_load_first_encapsulated - | Source "./include/vg/io/vpkg.hpp", line 401, in try_load_first_encapsulated - Source "./include/vg/io/vpkg.hpp", line 416, in _M_invoke [0x5583fa131a99] -#14 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583f9fe0320, in std::unique_ptr > vg::io::VPKG::try_load_encapsulated(vg::io::MessageIterator&) - | Source "./include/vg/io/vpkg.hpp", line 565, in operator() - Source "/usr/include/c++/14/bits/std_function.h", line 591, in try_load_encapsulated [0x5583f9fe0320] - 588: { - 589: if (_M_empty()) - 590: __throw_bad_function_call(); - > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); - 592: } - 593: - 594: #if __cpp_rtti -#13 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583fa9b751b, in std::_Function_handler, std::allocator > const&)> const&)> const&), vg::io::register_loader_saver_hash_graph()::{lambda(std::function, std::allocator > const&)> const&)> const&)#1}>::_M_invoke(std::_Any_data const&, std::function, std::allocator > const&)> const&)> const&) - | Source "/usr/include/c++/14/bits/std_function.h", line 290, in __invoke_r&, const std::function, std::allocator >&)>&)>&> - | 288: _M_invoke(const _Any_data& __functor, _ArgTypes&&... __args) - | 289: { - | > 290: return std::__invoke_r<_Res>(*_Base::_M_get_pointer(__functor), - | 291: std::forward<_ArgTypes>(__args)...); - | 292: } - | Source "/usr/include/c++/14/bits/invoke.h", line 138, in __invoke_impl&, const std::function, std::allocator >&)>&)>&> - | 136: #endif - | 137: using __tag = typename __result::__invoke_type; - | > 138: return std::__invoke_impl<__type>(__tag{}, std::forward<_Callable>(__fn), - | 139: std::forward<_Args>(__args)...); - | 140: } - | Source "/usr/include/c++/14/bits/invoke.h", line 61, in operator() - | 59: constexpr _Res - | 60: __invoke_impl(__invoke_other, _Fn&& __f, _Args&&... __args) - | > 61: { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); } - | 62: - | 63: template - Source "src/io/register_loader_saver_hash_graph.cpp", line 58, in _M_invoke [0x5583fa9b751b] -#12 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583fa9952bd, in vg::io::load_proto_to_graph(handlegraph::MutablePathMutableHandleGraph*, std::function, std::allocator > const&)> const&)> const&) - Source "src/io/load_proto_to_graph.cpp", line 35, in load_proto_to_graph [0x5583fa9952bd] -#11 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583fa994c1f, in vg::io::load_proto_to_graph(handlegraph::MutablePathMutableHandleGraph*, std::function const&)> const&) - | Source "src/io/load_proto_to_graph.cpp", line 76, in operator() - Source "/usr/include/c++/14/bits/std_function.h", line 591, in load_proto_to_graph [0x5583fa994c1f] - 588: { - 589: if (_M_empty()) - 590: __throw_bad_function_call(); - > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); - 592: } - 593: - 594: #if __cpp_rtti -#10 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583fa992605, in std::_Function_handler const&), vg::io::load_proto_to_graph(handlegraph::MutablePathMutableHandleGraph*, std::function, std::allocator > const&)> const&)> const&)::{lambda(std::function const&)#1}>::_M_invoke(std::_Any_data const&, std::function const&) - | Source "/usr/include/c++/14/bits/std_function.h", line 290, in __invoke_r&)>&, const std::function&> - | 288: _M_invoke(const _Any_data& __functor, _ArgTypes&&... __args) - | 289: { - | > 290: return std::__invoke_r<_Res>(*_Base::_M_get_pointer(__functor), - | 291: std::forward<_ArgTypes>(__args)...); - | 292: } - | Source "/usr/include/c++/14/bits/invoke.h", line 150, in __invoke_impl&)>&, const std::function&> - | 148: using __type = typename __result::type; - | 149: using __tag = typename __result::__invoke_type; - | > 150: std::__invoke_impl<__type>(__tag{}, std::forward<_Callable>(__fn), - | 151: std::forward<_Args>(__args)...); - | 152: } - | Source "/usr/include/c++/14/bits/invoke.h", line 61, in operator() - | 59: constexpr _Res - | 60: __invoke_impl(__invoke_other, _Fn&& __f, _Args&&... __args) - | > 61: { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); } - | 62: - | 63: template - | Source "src/io/load_proto_to_graph.cpp", line 37, in operator() - Source "/usr/include/c++/14/bits/std_function.h", line 591, in _M_invoke [0x5583fa992605] - 588: { - 589: if (_M_empty()) - 590: __throw_bad_function_call(); - > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); - 592: } - 593: - 594: #if __cpp_rtti -#9 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583f9fdc394, in std::_Function_handler, std::allocator > const&)> const&), vg::io::VPKG::try_load_encapsulated(vg::io::MessageIterator&)::{lambda(std::function, std::allocator > const&)> const&)#1}>::_M_invoke(std::_Any_data const&, std::function, std::allocator > const&)> const&) - | Source "/usr/include/c++/14/bits/std_function.h", line 290, in __invoke_r(vg::io::MessageIterator&)::&, const std::function, std::allocator >&)>&> - | 288: _M_invoke(const _Any_data& __functor, _ArgTypes&&... __args) - | 289: { - | > 290: return std::__invoke_r<_Res>(*_Base::_M_get_pointer(__functor), - | 291: std::forward<_ArgTypes>(__args)...); - | 292: } - | Source "/usr/include/c++/14/bits/invoke.h", line 150, in __invoke_impl(vg::io::MessageIterator&)::&, const std::function, std::allocator >&)>&> - | 148: using __type = typename __result::type; - | 149: using __tag = typename __result::__invoke_type; - | > 150: std::__invoke_impl<__type>(__tag{}, std::forward<_Callable>(__fn), - | 151: std::forward<_Args>(__args)...); - | 152: } - | Source "/usr/include/c++/14/bits/invoke.h", line 61, in operator() - | 59: constexpr _Res - | 60: __invoke_impl(__invoke_other, _Fn&& __f, _Args&&... __args) - | > 61: { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); } - | 62: - | 63: template - Source "./include/vg/io/vpkg.hpp", line 571, in _M_invoke [0x5583f9fdc394] -#8 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583fae06005, in vg::io::MessageIterator::operator++() - Source "./deps/libvgio/src/message_iterator.cpp", line 361, in operator++ [0x5583fae06005] -#7 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5583f995bd4e, in vg::io::MessageIterator::handle(bool, long, long) [clone .cold] - Source "./deps/libvgio/src/message_iterator.cpp", line 472, in handle [0x5583f995bd4e] -#6 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.33", at 0x7fe4324b3287, in __cxa_throw -#5 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.33", at 0x7fe4324a15e8, in std::terminate() -#4 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.33", at 0x7fe4324b3009, in -#3 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.33", at 0x7fe4324a1a3c, in -#2 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fe4322324ef, in abort -#1 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fe432249c41, in raise -#0 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fe43229dc8c, in -ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. -Please include this entire error log in your bug report! -━━━━━━━━━━━━━━━━━━━━ -[vg autoindex] Executing command: vg autoindex -p 1mb1kgp -w giraffe -P VG w/ Variant Paths:1mb1kgp.vg -P Giraffe Distance Index:1mb1kgp.dist -r 1mb1kgp/z.fa -v 1mb1kgp/z.vcf.gz -[IndexRegistry]: Checking for phasing in VCF(s). -[IndexRegistry]: Stripping allele paths from VG. -[W::bgzf_read_block] EOF marker is absent. The input may be truncated -terminate called after throwing an instance of 'std::runtime_error' - what(): [vg::io::MessageIterator] obsolete, invalid, or corrupt input at message 79256662206 group 79256662202 -━━━━━━━━━━━━━━━━━━━━ -Crash report for vg v1.59.0 "Casatico" -Stack trace (most recent call last) in thread 3281365: -#23 Object "/usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2", at 0xffffffffffffffff, in -#22 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fba0a91a677, in -#21 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fba0a89bf51, in -#20 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.33", at 0x7fba0aae0ea3, in -#19 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x562431dd5f43, in std::thread::_State_impl > >::_M_run() - | Source "/usr/include/c++/14/bits/std_thread.h", line 253, in operator() - | 252: void - | > 253: _M_run() { _M_func(); } - | 254: }; - | Source "/usr/include/c++/14/bits/std_thread.h", line 308, in _M_invoke<0> - | 306: using _Indices - | 307: = typename _Build_index_tuple::value>::__type; - | > 308: return _M_invoke(_Indices()); - | 309: } - | 310: }; - | Source "/usr/include/c++/14/bits/std_thread.h", line 301, in __invoke > - | 299: typename __result<_Tuple>::type - | 300: _M_invoke(_Index_tuple<_Ind...>) - | > 301: { return std::__invoke(std::get<_Ind>(std::move(_M_t))...); } - | 302: - | 303: typename __result<_Tuple>::type - | Source "/usr/include/c++/14/bits/invoke.h", line 96, in __invoke_impl > - | 94: using __type = typename __result::type; - | 95: using __tag = typename __result::__invoke_type; - | > 96: return std::__invoke_impl<__type>(__tag{}, std::forward<_Callable>(__fn), - | 97: std::forward<_Args>(__args)...); - | 98: } - | Source "/usr/include/c++/14/bits/invoke.h", line 61, in operator() - | 59: constexpr _Res - | 60: __invoke_impl(__invoke_other, _Fn&& __f, _Args&&... __args) - | > 61: { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); } - | 62: - | 63: template - | Source "src/job_schedule.cpp", line 77, in operator() - Source "/usr/include/c++/14/bits/std_function.h", line 591, in _M_run [0x562431dd5f43] - 588: { - 589: if (_M_empty()) - 590: __throw_bad_function_call(); - > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); - 592: } - 593: - 594: #if __cpp_rtti -#18 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x562431d9013a, in vg::VGIndexes::get_vg_index_registry()::{lambda(std::vector > const&, vg::IndexingPlan const*, std::set, std::allocator >, std::less, std::allocator > >, std::allocator, std::allocator > > > const&)#1}::operator()(std::vector > const&, vg::IndexingPlan const*, std::set, std::allocator >, std::less, std::allocator > >, std::allocator, std::allocator > > > const&) const::{lambda(long)#1}::operator()(long) const - Source "src/index_registry.cpp", line 1752, in operator() [0x562431d9013a] -#17 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x562431dbe043, in std::unique_ptr > vg::io::VPKG::load_one(std::istream&, std::__cxx11::basic_string, std::allocator > const&) - | Source "./include/vg/io/vpkg.hpp", line 187, in try_load_one - Source "./include/vg/io/vpkg.hpp", line 135, in load_one [0x562431dbe043] -#16 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5624318e7fde, in vg::io::VPKG::with_putback(std::istream&, std::function const&) - | Source "./include/vg/io/vpkg.hpp", line 595, in operator() - Source "/usr/include/c++/14/bits/std_function.h", line 591, in with_putback [0x5624318e7fde] - 588: { - 589: if (_M_empty()) - 590: __throw_bad_function_call(); - > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); - 592: } - 593: - 594: #if __cpp_rtti -#15 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x562431922357, in std::_Function_handler(std::istream&, std::__cxx11::basic_string, std::allocator > const&)::{lambda(std::istream&)#1}>::_M_invoke(std::_Any_data const&, std::istream&) - | Source "/usr/include/c++/14/bits/std_function.h", line 290, in __invoke_r(std::istream&, const std::string&)::&, std::basic_istream >&> - | 288: _M_invoke(const _Any_data& __functor, _ArgTypes&&... __args) - | 289: { - | > 290: return std::__invoke_r<_Res>(*_Base::_M_get_pointer(__functor), - | 291: std::forward<_ArgTypes>(__args)...); - | 292: } - | Source "/usr/include/c++/14/bits/invoke.h", line 150, in __invoke_impl(std::istream&, const std::string&)::&, std::basic_istream >&> - | 148: using __type = typename __result::type; - | 149: using __tag = typename __result::__invoke_type; - | > 150: std::__invoke_impl<__type>(__tag{}, std::forward<_Callable>(__fn), - | 151: std::forward<_Args>(__args)...); - | 152: } - | Source "/usr/include/c++/14/bits/invoke.h", line 61, in operator() - | 59: constexpr _Res - | 60: __invoke_impl(__invoke_other, _Fn&& __f, _Args&&... __args) - | > 61: { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); } - | 62: - | 63: template - | Source "./include/vg/io/vpkg.hpp", line 135, in operator() - | Source "./include/vg/io/vpkg.hpp", line 141, in try_load_encapsulated - | Source "./include/vg/io/vpkg.hpp", line 482, in with_putback - | Source "./include/vg/io/vpkg.hpp", line 595, in operator() - Source "/usr/include/c++/14/bits/std_function.h", line 591, in _M_invoke [0x562431922357] - 588: { - 589: if (_M_empty()) - 590: __throw_bad_function_call(); - > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); - 592: } - 593: - 594: #if __cpp_rtti -#14 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5624319246ff, in std::_Function_handler(std::istream&)::{lambda(std::istream&)#1}>::_M_invoke(std::_Any_data const&, std::istream&) - | Source "/usr/include/c++/14/bits/std_function.h", line 290, in __invoke_r(std::istream&)::&, std::basic_istream >&> - | 288: _M_invoke(const _Any_data& __functor, _ArgTypes&&... __args) - | 289: { - | > 290: return std::__invoke_r<_Res>(*_Base::_M_get_pointer(__functor), - | 291: std::forward<_ArgTypes>(__args)...); - | 292: } - | Source "/usr/include/c++/14/bits/invoke.h", line 150, in __invoke_impl(std::istream&)::&, std::basic_istream >&> - | 148: using __type = typename __result::type; - | 149: using __tag = typename __result::__invoke_type; - | > 150: std::__invoke_impl<__type>(__tag{}, std::forward<_Callable>(__fn), - | 151: std::forward<_Args>(__args)...); - | 152: } - | Source "/usr/include/c++/14/bits/invoke.h", line 61, in operator() - | 59: constexpr _Res - | 60: __invoke_impl(__invoke_other, _Fn&& __f, _Args&&... __args) - | > 61: { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); } - | 62: - | 63: template - | Source "./include/vg/io/vpkg.hpp", line 526, in try_load_encapsulated - | Source "./include/vg/io/vpkg.hpp", line 565, in operator() - Source "/usr/include/c++/14/bits/std_function.h", line 591, in _M_invoke [0x5624319246ff] - 588: { - 589: if (_M_empty()) - 590: __throw_bad_function_call(); - > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); - 592: } - 593: - 594: #if __cpp_rtti -#13 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5624322c251b, in std::_Function_handler, std::allocator > const&)> const&)> const&), vg::io::register_loader_saver_hash_graph()::{lambda(std::function, std::allocator > const&)> const&)> const&)#1}>::_M_invoke(std::_Any_data const&, std::function, std::allocator > const&)> const&)> const&) - | Source "/usr/include/c++/14/bits/std_function.h", line 290, in __invoke_r&, const std::function, std::allocator >&)>&)>&> - | 288: _M_invoke(const _Any_data& __functor, _ArgTypes&&... __args) - | 289: { - | > 290: return std::__invoke_r<_Res>(*_Base::_M_get_pointer(__functor), - | 291: std::forward<_ArgTypes>(__args)...); - | 292: } - | Source "/usr/include/c++/14/bits/invoke.h", line 138, in __invoke_impl&, const std::function, std::allocator >&)>&)>&> - | 136: #endif - | 137: using __tag = typename __result::__invoke_type; - | > 138: return std::__invoke_impl<__type>(__tag{}, std::forward<_Callable>(__fn), - | 139: std::forward<_Args>(__args)...); - | 140: } - | Source "/usr/include/c++/14/bits/invoke.h", line 61, in operator() - | 59: constexpr _Res - | 60: __invoke_impl(__invoke_other, _Fn&& __f, _Args&&... __args) - | > 61: { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); } - | 62: - | 63: template - Source "src/io/register_loader_saver_hash_graph.cpp", line 58, in _M_invoke [0x5624322c251b] -#12 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5624322a02bd, in vg::io::load_proto_to_graph(handlegraph::MutablePathMutableHandleGraph*, std::function, std::allocator > const&)> const&)> const&) - Source "src/io/load_proto_to_graph.cpp", line 35, in load_proto_to_graph [0x5624322a02bd] -#11 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x56243229fc1f, in vg::io::load_proto_to_graph(handlegraph::MutablePathMutableHandleGraph*, std::function const&)> const&) - | Source "src/io/load_proto_to_graph.cpp", line 76, in operator() - Source "/usr/include/c++/14/bits/std_function.h", line 591, in load_proto_to_graph [0x56243229fc1f] - 588: { - 589: if (_M_empty()) - 590: __throw_bad_function_call(); - > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); - 592: } - 593: - 594: #if __cpp_rtti -#10 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x56243229d605, in std::_Function_handler const&), vg::io::load_proto_to_graph(handlegraph::MutablePathMutableHandleGraph*, std::function, std::allocator > const&)> const&)> const&)::{lambda(std::function const&)#1}>::_M_invoke(std::_Any_data const&, std::function const&) - | Source "/usr/include/c++/14/bits/std_function.h", line 290, in __invoke_r&)>&, const std::function&> - | 288: _M_invoke(const _Any_data& __functor, _ArgTypes&&... __args) - | 289: { - | > 290: return std::__invoke_r<_Res>(*_Base::_M_get_pointer(__functor), - | 291: std::forward<_ArgTypes>(__args)...); - | 292: } - | Source "/usr/include/c++/14/bits/invoke.h", line 150, in __invoke_impl&)>&, const std::function&> - | 148: using __type = typename __result::type; - | 149: using __tag = typename __result::__invoke_type; - | > 150: std::__invoke_impl<__type>(__tag{}, std::forward<_Callable>(__fn), - | 151: std::forward<_Args>(__args)...); - | 152: } - | Source "/usr/include/c++/14/bits/invoke.h", line 61, in operator() - | 59: constexpr _Res - | 60: __invoke_impl(__invoke_other, _Fn&& __f, _Args&&... __args) - | > 61: { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); } - | 62: - | 63: template - | Source "src/io/load_proto_to_graph.cpp", line 37, in operator() - Source "/usr/include/c++/14/bits/std_function.h", line 591, in _M_invoke [0x56243229d605] - 588: { - 589: if (_M_empty()) - 590: __throw_bad_function_call(); - > 591: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...); - 592: } - 593: - 594: #if __cpp_rtti -#9 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x5624319220a4, in std::_Function_handler, std::allocator > const&)> const&), vg::io::VPKG::try_load_encapsulated(vg::io::MessageIterator&)::{lambda(std::function, std::allocator > const&)> const&)#1}>::_M_invoke(std::_Any_data const&, std::function, std::allocator > const&)> const&) - | Source "/usr/include/c++/14/bits/std_function.h", line 290, in __invoke_r(vg::io::MessageIterator&)::&, const std::function, std::allocator >&)>&> - | 288: _M_invoke(const _Any_data& __functor, _ArgTypes&&... __args) - | 289: { - | > 290: return std::__invoke_r<_Res>(*_Base::_M_get_pointer(__functor), - | 291: std::forward<_ArgTypes>(__args)...); - | 292: } - | Source "/usr/include/c++/14/bits/invoke.h", line 150, in __invoke_impl(vg::io::MessageIterator&)::&, const std::function, std::allocator >&)>&> - | 148: using __type = typename __result::type; - | 149: using __tag = typename __result::__invoke_type; - | > 150: std::__invoke_impl<__type>(__tag{}, std::forward<_Callable>(__fn), - | 151: std::forward<_Args>(__args)...); - | 152: } - | Source "/usr/include/c++/14/bits/invoke.h", line 61, in operator() - | 59: constexpr _Res - | 60: __invoke_impl(__invoke_other, _Fn&& __f, _Args&&... __args) - | > 61: { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); } - | 62: - | 63: template - Source "./include/vg/io/vpkg.hpp", line 571, in _M_invoke [0x5624319220a4] -#8 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x562432711005, in vg::io::MessageIterator::operator++() - Source "./deps/libvgio/src/message_iterator.cpp", line 361, in operator++ [0x562432711005] -#7 Object "/build/reproducible-path/vg-1.59.0+ds/debian/help/vg", at 0x562431266d4e, in vg::io::MessageIterator::handle(bool, long, long) [clone .cold] - Source "./deps/libvgio/src/message_iterator.cpp", line 472, in handle [0x562431266d4e] -#6 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.33", at 0x7fba0aab3287, in __cxa_throw -#5 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.33", at 0x7fba0aaa15e8, in std::terminate() -#4 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.33", at 0x7fba0aab3009, in -#3 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.33", at 0x7fba0aaa1a3c, in -#2 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fba0a8324ef, in abort -#1 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fba0a849c41, in raise -#0 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7fba0a89dc8c, in -ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. -Please include this entire error log in your bug report! -━━━━━━━━━━━━━━━━━━━━ -error:[vg giraffe] Couldn't open GBZ file 1mb1kgp.giraffe.gbz +not ok 6 - vg depth of paths reports just path with selected prefix +# got: '0' +# expected: '1' +Failed 5/6 subtests +t/50_vg_giraffe.t: line 10: 3289052 Illegal instruction vg construct -a -r small/x.fa -v small/x.vcf.gz > x.vg +t/50_vg_giraffe.t: line 11: 3289053 Illegal instruction vg index -x x.xg x.vg +t/50_vg_giraffe.t: line 12: 3289054 Illegal instruction vg gbwt -o x-haps.gbwt -x x.vg -v small/x.vcf.gz +t/50_vg_giraffe.t: line 13: 3289055 Illegal instruction vg gbwt -o x-paths.gbwt -x x.vg --index-paths +t/50_vg_giraffe.t: line 14: 3289056 Illegal instruction vg gbwt -o x-merged.gbwt -m x-haps.gbwt x-paths.gbwt +t/50_vg_giraffe.t: line 15: 3289057 Illegal instruction vg gbwt -o x.gbwt --augment-gbwt -x x.vg x-merged.gbwt +t/50_vg_giraffe.t: line 16: 3289058 Illegal instruction vg index -j x.dist x.vg +t/50_vg_giraffe.t: line 17: 3289059 Illegal instruction vg minimizer -k 29 -w 11 -d x.dist -g x.gbwt -o x.min x.xg +t/50_vg_giraffe.t: line 19: 3289060 Illegal instruction vg giraffe -x x.xg -H x.gbwt -m x.min -d x.dist -f reads/small.middle.ref.fq > mapped1.gam +t/50_vg_giraffe.t: line 23: 3289062 Illegal instruction vg giraffe -Z x.giraffe.gbz -m x.min -d x.dist -f reads/small.middle.ref.fq > mapped1.gam +t/50_vg_giraffe.t: line 27: 3289064 Illegal instruction vg gbwt -x x.xg -g x.gg x.gbwt +t/50_vg_giraffe.t: line 28: 3289065 Illegal instruction vg giraffe -g x.gg -H x.gbwt -m x.min -d x.dist -f reads/small.middle.ref.fq > mapped1.gam +t/50_vg_giraffe.t: line 32: 3289067 Illegal instruction vg giraffe -Z x.giraffe.gbz -d x.dist -f reads/small.middle.ref.fq > mapped1.gam +t/50_vg_giraffe.t: line 35: 3289068 Illegal instruction vg giraffe -Z x.giraffe.gbz -f reads/small.middle.ref.fq > mapped1.gam +t/50_vg_giraffe.t: line 42: 3289076 Illegal instruction vg giraffe -Z x.giraffe.gbz -f reads/small.middle.ref.fq -b fast > /dev/null +t/50_vg_giraffe.t: line 45: 3289077 Illegal instruction vg giraffe -Z x.giraffe.gbz -f reads/small.middle.ref.fq -b default > /dev/null +t/50_vg_giraffe.t: line 48: 3289078 Illegal instruction vg giraffe -Z x.giraffe.gbz -f reads/small.middle.ref.fq --full-l-bonus 0 > mapped-nobonus.gam +t/50_vg_giraffe.t: line 52: 3289083 Illegal instruction vg minimizer -k 29 -b -s 18 -d x.dist -g x.gbwt -o x.sync x.xg +t/50_vg_giraffe.t: line 54: 3289084 Illegal instruction vg giraffe -x x.xg -H x.gbwt -m x.sync -d x.dist -f reads/small.middle.ref.fq > mapped.sync.gam +chmod: cannot access 'x.dist': No such file or directory +t/50_vg_giraffe.t: line 58: 3289086 Illegal instruction vg giraffe -x x.xg -H x.gbwt -m x.min -d x.dist -f reads/small.middle.ref.fq > /dev/null +t/50_vg_giraffe.t: line 66: 3289097 Illegal instruction vg giraffe -x x.xg -H x.gbwt -m x.min -d x.dist -f read.fq > read.gam +t/50_vg_giraffe.t: line 79: 3289108 Illegal instruction vg giraffe x.fa x.vcf.gz -f reads/small.middle.ref.fq > mapped2.gam +t/50_vg_giraffe.t: line 104: 3289122 Illegal instruction vg giraffe x.fa x.vcf.gz -f small/x.fa_1.fastq > single.gam +t/50_vg_giraffe.t: line 107: 3289127 Illegal instruction vg giraffe x.fa x.vcf.gz -f small/x.fa_1.fastq -f small/x.fa_1.fastq --fragment-mean 300 --fragment-stdev 100 > paired.gam +t/50_vg_giraffe.t: line 111: 3289133 Illegal instruction vg giraffe x.fa x.vcf.gz -iG <(vg view -a small/x-s13241-n1-p500-v300.gam | sed 's%_1%/1%' | sed 's%_2%/2%' | vg view -JaG -) --output-format SAM > surjected.sam +t/50_vg_giraffe.t: line 119: 3289169 Illegal instruction vg giraffe x.fa x.vcf.gz -G <(vg view -a small/x-s13241-n1-p500-v300.gam | sed 's%_1%/1%' | sed 's%_2%/2%' | vg view -JaG -) --output-format SAM > surjected.sam +t/50_vg_giraffe.t: line 144: 3289217 Illegal instruction vg construct -r small/x.fa > x.vg +t/50_vg_giraffe.t: line 145: 3289218 Illegal instruction vg sim -a -p 200 -v 10 -l 50 -n 1000 -s 12345 -x x.vg > x.gam +t/50_vg_giraffe.t: line 147: 3289219 Illegal instruction vg giraffe xy.fa xy.vcf.gz -G x.gam -o SAM -i --fragment-mean 200 --fragment-stdev 10 --distance-limit 50 > xy.sam +t/50_vg_giraffe.t: line 156: 3289226 Illegal instruction vg giraffe xy.fa xy.vcf.gz -G x.gam -o SAM > xy.sam +t/50_vg_giraffe.t: line 165: 3289233 Illegal instruction vg giraffe xy.fa xy.vcf.gz -G x.gam --track-provenance --discard +t/50_vg_giraffe.t: line 168: 3289234 Illegal instruction vg giraffe xy.fa xy.vcf.gz -G x.gam --track-provenance --track-correctness -o json > xy.json +t/50_vg_giraffe.t: line 173: 3289239 Illegal instruction vg giraffe xy.fa xy.vcf.gz -G x.gam -i --fragment-mean 200 --fragment-stdev 10 --distance-limit 50 --track-provenance --discard +t/50_vg_giraffe.t: line 176: 3289240 Illegal instruction vg giraffe xy.fa xy.vcf.gz -G x.gam -i --fragment-mean 200 --fragment-stdev 10 --distance-limit 50 --track-provenance --track-correctness -o json > xy.json +t/50_vg_giraffe.t: line 185: 3289251 Illegal instruction vg giraffe -Z xy.giraffe.gbz -G x.gam -o BAM > xy.bam +[main_samview] fail to read the header from "xy.bam". +t/50_vg_giraffe.t: line 192: 3289257 Illegal instruction vg autoindex -p brca -w giraffe -g graphs/cactus-BRCA2.gfa +t/50_vg_giraffe.t: line 193: 3289258 Illegal instruction vg sim -s 100 -x brca.giraffe.gbz -n 200 -a > reads.gam +t/50_vg_giraffe.t: line 194: 3289259 Illegal instruction vg giraffe -Z brca.giraffe.gbz -m brca.min -d brca.dist -G reads.gam --named-coordinates > mapped.gam +t/50_vg_giraffe.t: line 199: 3289271 Illegal instruction vg giraffe -Z brca.giraffe.gbz -m brca.min -d brca.dist -G reads.gam --named-coordinates -o gaf > mapped.gaf +t/50_vg_giraffe.t: line 210: 3289289 Illegal instruction vg construct -S -a -r 1mb1kgp/z.fa -v 1mb1kgp/z.vcf.gz > 1mb1kgp.vg 2> /dev/null +t/50_vg_giraffe.t: line 211: 3289290 Illegal instruction vg index -j 1mb1kgp.dist 1mb1kgp.vg +t/50_vg_giraffe.t: line 212: 3289291 Illegal instruction vg autoindex -p 1mb1kgp -w giraffe -P "VG w/ Variant Paths:1mb1kgp.vg" -P "Giraffe Distance Index:1mb1kgp.dist" -r 1mb1kgp/z.fa -v 1mb1kgp/z.vcf.gz +t/50_vg_giraffe.t: line 213: 3289292 Illegal instruction vg giraffe -Z 1mb1kgp.giraffe.gbz -f reads/1mb1kgp_longread.fq -U 300 --progress --track-provenance --align-from-chains > longread.gam t/50_vg_giraffe.t ..... 1..50 -ok 1 - a read can be mapped with xg + gbwt + min + dist specified without crashing -ok 2 - a read can be mapped with gbz + min + dist specified without crashing -ok 3 - a read can be mapped with gg + gbwt + min + dist specified without crashing -ok 4 - a read can be mapped with the minimizer index being regenerated -ok 5 - a read can be mapped with the indexes being inferred by name -ok 6 - Mapping logs runtime per read -ok 7 - Mapping produces the correct score -ok 8 - a read can be mapped with the fast preset -ok 9 - a read can be mapped with the default preset -ok 10 - Mapping without a full length bonus produces the correct score -ok 11 - a read can be mapped with syncmer indexes without crashing -ok 12 - a read can be mapped when the distance index is not writable +not ok 1 - a read can be mapped with xg + gbwt + min + dist specified without crashing +# got: '132' +# expected: '0' +not ok 2 - a read can be mapped with gbz + min + dist specified without crashing +# got: '132' +# expected: '0' +not ok 3 - a read can be mapped with gg + gbwt + min + dist specified without crashing +# got: '132' +# expected: '0' +not ok 4 - a read can be mapped with the minimizer index being regenerated +# got: '132' +# expected: '0' +not ok 5 - a read can be mapped with the indexes being inferred by name +# got: '132' +# expected: '0' +not ok 6 - Mapping logs runtime per read +# got: '0' +# expected: '1' +not ok 7 - Mapping produces the correct score +# got: '' +# expected: '73' +not ok 8 - a read can be mapped with the fast preset +# got: '132' +# expected: '0' +not ok 9 - a read can be mapped with the default preset +# got: '132' +# expected: '0' +not ok 10 - Mapping without a full length bonus produces the correct score +# got: '' +# expected: '63' +not ok 11 - a read can be mapped with syncmer indexes without crashing +# got: '132' +# expected: '0' +not ok 12 - a read can be mapped when the distance index is not writable +# got: '132' +# expected: '0' ok 13 - a read which softclips does not appear to loop -ok 14 - a read can be mapped with just FASTA and VCF without crashing -ok 15 - mapping with just a FASTA and a VCF produced JSON-able alignments +not ok 14 - a read can be mapped with just FASTA and VCF without crashing +# got: '132' +# expected: '0' +not ok 15 - mapping with just a FASTA and a VCF produced JSON-able alignments +# got: '1' +# expected: '0' ok 16 - mapping to manually-generated indexes and automatically-generated indexes is the same ok 17 - mapping with syncmers produces the same alignment as mapping with minimizers -ok 18 - unpaired reads lack cross-references +not ok 18 - unpaired reads lack cross-references +# got: '0' +# expected: '1000' ok 19 - paired reads have cross-references -ok 20 - surjection of paired reads to SAM yields correct positions -ok 21 - surjection of paired reads to SAM yields correct pair partner positions -ok 22 - surjection of paired reads to SAM yields properly matched QNAMEs -ok 23 - surjection of paired reads to SAM produces correct pair partner contigs -ok 24 - surjection of paired reads to SAM produces correct flags -ok 25 - surjection of unpaired reads to SAM yields correct positions -ok 26 - surjection of unpaired reads to SAM yields correct pair partner positions -ok 27 - surjection of unpaired reads to SAM yields distinct QNAMEs -ok 28 - surjection of unpaired reads to SAM produces absent partner contigs -ok 29 - surjection of unpaired reads to SAM produces correct flags -ok 30 - surjecting with a sequence dictionary in non-sorted order produces headers in non-sorted order -ok 31 - surjecting with a sequence dictionary in sorted order produces headers in sorted order -ok 32 - paired reads are evenly split between equivalent mappings -ok 33 - unpaired reads are evenly split between equivalent mappings -ok 34 - provenance tracking succeeds for unpaired reads -ok 35 - correctness tracking succeeds for unpaired reads -ok 36 - unpaired reads are annotated with minimizer coverage -ok 37 - provenance tracking succeeds for paired reads -ok 38 - correctness tracking succeeds for paired reads -ok 39 - paired reads are annotated with minimizer coverage -ok 40 - paired reads all have nonzero correct minimizer coverage -ok 41 - vg giraffe can map to BAM using a GBZ alone -ok 42 - GBZ-based BAM contains the expected number of reads -ok 43 - Mapping reads to named coordinates on a nontrivial graph without walks succeeds -ok 44 - Reads are all mapped +not ok 20 - surjection of paired reads to SAM yields correct positions +# got: '' +# expected: '321 +# 762' +not ok 21 - surjection of paired reads to SAM yields correct pair partner positions +# got: '' +# expected: '762 +# 321' +not ok 22 - surjection of paired reads to SAM yields properly matched QNAMEs +# got: '0' +# expected: '1' +not ok 23 - surjection of paired reads to SAM produces correct pair partner contigs +# got: '' +# expected: '= +# =' +not ok 24 - surjection of paired reads to SAM produces correct flags +# got: '' +# expected: '163 +# 83' +not ok 25 - surjection of unpaired reads to SAM yields correct positions +# got: '' +# expected: '321 +# 762' +not ok 26 - surjection of unpaired reads to SAM yields correct pair partner positions +# got: '' +# expected: '0 +# 0' +not ok 27 - surjection of unpaired reads to SAM yields distinct QNAMEs +# got: '0' +# expected: '2' +not ok 28 - surjection of unpaired reads to SAM produces absent partner contigs +# got: '' +# expected: '* +# *' +not ok 29 - surjection of unpaired reads to SAM produces correct flags +# got: '' +# expected: '0 +# 16' +0a1,3 +> @HD VN:1.5 SO:unknown +> @SQ SN:y LN:1001 +> @SQ SN:x LN:1001 +not ok 30 - surjecting with a sequence dictionary in non-sorted order produces headers in non-sorted order +# got: '1' +# expected: '0' +0a1,3 +> @HD VN:1.5 SO:unknown +> @SQ SN:x LN:1001 +> @SQ SN:y LN:1001 +not ok 31 - surjecting with a sequence dictionary in sorted order produces headers in sorted order +# got: '1' +# expected: '0' +not ok 32 - paired reads are evenly split between equivalent mappings +# got: '0' +# expected: '1' +not ok 33 - unpaired reads are evenly split between equivalent mappings +# got: '0' +# expected: '1' +not ok 34 - provenance tracking succeeds for unpaired reads +# got: '132' +# expected: '0' +not ok 35 - correctness tracking succeeds for unpaired reads +# got: '132' +# expected: '0' +not ok 36 - unpaired reads are annotated with minimizer coverage +# got: '0' +# expected: '2000' +not ok 37 - provenance tracking succeeds for paired reads +# got: '132' +# expected: '0' +not ok 38 - correctness tracking succeeds for paired reads +# got: '132' +# expected: '0' +not ok 39 - paired reads are annotated with minimizer coverage +# got: '0' +# expected: '2000' +not ok 40 - paired reads all have nonzero correct minimizer coverage +# got: '0' +# expected: '2000' +not ok 41 - vg giraffe can map to BAM using a GBZ alone +# got: '132' +# expected: '0' +not ok 42 - GBZ-based BAM contains the expected number of reads +# got: '0' +# expected: '2000' +not ok 43 - Mapping reads to named coordinates on a nontrivial graph without walks succeeds +# got: '132' +# expected: '0' +not ok 44 - Reads are all mapped +# got: '0' +# expected: '200' ok 45 - GFA segment names are all set -ok 46 - Mapping reads as GAF to named coordinates on a nontrivial graph without walks succeeds +not ok 46 - Mapping reads as GAF to named coordinates on a nontrivial graph without walks succeeds +# got: '132' +# expected: '0' ok 47 - Mapping reads as named GAF uses the same names as named GAM not ok 48 - A long read can be correctly aligned # got: '' @@ -23537,457 +29674,573 @@ not ok 50 - Long read minimizer set is correctly restricted # got: '0' # expected: '1' -Failed 3/50 subtests -[vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. +Failed 44/50 subtests +t/51_vg_combine.t: line 10: 3289306 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz > x.vg +t/51_vg_combine.t: line 11: 3289307 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz + 3289308 | vg paths -d -v - > y.vg +t/51_vg_combine.t: line 12: 3289309 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz + 3289310 | vg paths -d -v - > z.vg +t/51_vg_combine.t: line 14: 3289311 Illegal instruction vg combine x.vg y.vg z.vg > xyz.vg +t/51_vg_combine.t: line 18: 3289320 Illegal instruction vg paths -Ev x.vg > x.paths +t/51_vg_combine.t: line 19: 3289321 Illegal instruction vg paths -Ev xyz.vg > xyz.paths +t/51_vg_combine.t: line 25: 3289324 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz + 3289325 | vg convert -p - > x.vg +t/51_vg_combine.t: line 26: 3289326 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz + 3289327 | vg paths -d -v - + 3289328 | vg convert -a - > y.vg +t/51_vg_combine.t: line 27: 3289329 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz + 3289330 | vg paths -d -v - + 3289331 | vg convert -p - > z.vg +t/51_vg_combine.t: line 29: 3289332 Illegal instruction vg combine x.vg y.vg z.vg > xyz.vg +t/51_vg_combine.t: line 33: 3289341 Illegal instruction vg paths -Ev x.vg > x.paths +t/51_vg_combine.t: line 34: 3289342 Illegal instruction vg paths -Ev xyz.vg > xyz.paths +t/51_vg_combine.t: line 40: 3289345 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz + 3289346 | vg convert -p - > x.vg +t/51_vg_combine.t: line 41: 3289347 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz + 3289348 | vg convert -a - > y.vg +t/51_vg_combine.t: line 42: 3289349 Illegal instruction vg construct -r small/x.fa -v small/x.vcf.gz + 3289350 | vg convert -v - > z.vg +t/51_vg_combine.t: line 44: 3289351 Illegal instruction vg combine -p x.vg y.vg z.vg > xyz.vg t/51_vg_combine.t ..... 1..10 -ok 1 - combined graph as correct total nodes -ok 2 - combined graph as correct total edges +not ok 1 - unnamed test +# got: '645' +# expected: 'combined graph as correct total nodes' +not ok 2 - unnamed test +# got: '888' +# expected: 'combined graph as correct total edges' ok 3 - combined graph has same input path -ok 4 - combined handle graph as correct total nodes -ok 5 - combined handle graph as correct total edges +not ok 4 - unnamed test +# got: '645' +# expected: 'combined handle graph as correct total nodes' +not ok 5 - unnamed test +# got: '888' +# expected: 'combined handle graph as correct total edges' ok 6 - combined handle graph has same input path -ok 7 - path combined graph as correct total nodes -ok 8 - path combined path graph as correct total edges -ok 9 - path combined graph as correct number of paths -ok 10 - combined path has correct size -ok +not ok 7 - unnamed test +# got: '645' +# expected: 'path combined graph as correct total nodes' +not ok 8 - unnamed test +# got: '890' +# expected: 'path combined path graph as correct total edges' +not ok 9 - path combined graph as correct number of paths +# got: '0' +# expected: '1' +not ok 10 - unnamed test +# got: '3003' +# expected: 'combined path has correct size' +Failed 8/10 subtests +rm: cannot remove 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 12: 3289369 Illegal instruction vg autoindex -p auto -w map -r tiny/tiny.fa -v tiny/tiny.vcf.gz --force-unphased +ls: cannot access 'auto.*': No such file or directory +ls: cannot access 'auto.xg': No such file or directory +ls: cannot access 'auto.gcsa*': No such file or directory +t/52_vg_autoindex.t: line 17: 3289380 Illegal instruction vg sim -x auto.xg -n 20 -a -l 10 + 3289381 | vg map -d auto -t 1 -G - > /dev/null +rm: cannot remove 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 22: 3289384 Illegal instruction vg autoindex -p auto -w map -r small/x.fa -v small/x.vcf.gz -r small/y.fa -v small/y.vcf.gz +t/52_vg_autoindex.t: line 24: 3289386 Illegal instruction vg sim -x auto.xg -n 20 -a -l 10 + 3289387 | vg map -d auto -t 1 -G - > /dev/null +rm: cannot remove 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 29: 3289390 Illegal instruction vg autoindex -p auto -w map -r small/xy.fa -v small/xy2.vcf.gz +t/52_vg_autoindex.t: line 31: 3289392 Illegal instruction vg sim -x auto.xg -n 20 -a -l 10 + 3289393 | vg map -d auto -t 1 -G - > /dev/null +rm: cannot remove 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 36: 3289396 Illegal instruction vg autoindex -p auto -w mpmap -w rpvg -r tiny/tiny.fa -v tiny/tiny.vcf.gz -x tiny/tiny.gtf +ls: cannot access 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 39: 3289401 Illegal instruction vg sim -x auto.spliced.xg -n 20 -a -l 10 + 3289402 | vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - > /dev/null +cat: auto.txorigin.tsv: No such file or directory +rm: cannot remove 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 46: 3289411 Illegal instruction vg autoindex -p auto -w mpmap -r tiny/tiny.fa -v tiny/tiny.vcf.gz -x tiny/tiny.gtf --force-unphased +ls: cannot access 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 49: 3289416 Illegal instruction vg sim -x auto.spliced.xg -n 20 -a -l 10 + 3289417 | vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - > /dev/null +rm: cannot remove 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 54: 3289420 Illegal instruction vg autoindex -p auto -w mpmap -r tiny/tiny.fa -x tiny/tiny.gtf +ls: cannot access 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 57: 3289425 Illegal instruction vg sim -x auto.spliced.xg -n 20 -a -l 10 + 3289426 | vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - > /dev/null +rm: cannot remove 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 62: 3289429 Illegal instruction vg autoindex -p auto -w mpmap -w rpvg -r small/x.fa -r small/y.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/x.gtf -x small/y.gtf +ls: cannot access 'auto.*': No such file or directory +rm: cannot remove 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 68: 3289435 Illegal instruction vg autoindex -p auto -w mpmap -r small/x.fa -r small/y.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/x.gtf -x small/y.gtf --force-unphased +ls: cannot access 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 71: 3289440 Illegal instruction vg sim -x auto.spliced.xg -n 20 -a -l 10 + 3289441 | vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - > /dev/null +rm: cannot remove 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 76: 3289444 Illegal instruction 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 +rm: cannot remove 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 81: 3289447 Illegal instruction vg autoindex -p auto -w mpmap -w rpvg -r small/xy.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/xy.gtf +rm: cannot remove 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 86: 3289450 Illegal instruction vg autoindex -p auto -w mpmap -g graphs/gfa_with_w_lines.gfa -x graphs/gfa_with_w_lines.gtf +t/52_vg_autoindex.t: line 88: 3289452 Illegal instruction vg sim -x auto.spliced.xg -n 20 -a -l 5 + 3289453 | vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - > /dev/null +rm: cannot remove 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 93: 3289456 Illegal instruction vg autoindex -p auto -w mpmap -g graphs/gfa_with_w_lines.gfa -x graphs/gfa_with_w_lines.gtf -H graphs/gfa_with_w_lines_haplo.gtf +t/52_vg_autoindex.t: line 95: 3289458 Illegal instruction vg sim -x auto.spliced.xg -n 20 -a -l 5 + 3289459 | vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - > /dev/null +rm: cannot remove 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 100: 3289462 Illegal instruction vg autoindex -p auto -w rpvg -w mpmap -g graphs/gfa_with_w_lines.gfa -x graphs/gfa_with_w_lines.gtf +rm: cannot remove 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 105: 3289465 Illegal instruction vg autoindex -p auto -w rpvg -w mpmap -g graphs/gfa_with_w_lines.gfa -x graphs/gfa_with_w_lines.gtf -H graphs/gfa_with_w_lines_haplo.gtf +rm: cannot remove 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 110: 3289468 Illegal instruction vg autoindex -p auto -w giraffe -r tiny/tiny.fa -v tiny/tiny.vcf.gz +ls: cannot access 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 113: 3289473 Illegal instruction vg construct -r tiny/tiny.fa -v tiny/tiny.vcf.gz > t.vg +t/52_vg_autoindex.t: line 114: 3289474 Illegal instruction vg index -x t.xg t.vg +t/52_vg_autoindex.t: line 115: 3289475 Illegal instruction vg sim -x t.xg -n 20 -a -l 10 + 3289476 | vg giraffe -Z auto.giraffe.gbz -m auto.min -d auto.dist -G - > /dev/null +rm: cannot remove 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 121: 3289480 Illegal instruction vg autoindex -p auto -w giraffe -g graphs/gfa_with_w_lines.gfa +ls: cannot access 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 124: 3289485 Illegal instruction vg convert -g graphs/gfa_with_w_lines.gfa -x > g.xg +t/52_vg_autoindex.t: line 125: 3289486 Illegal instruction vg sim -x g.xg -n 20 -a -l 4 + 3289487 | vg giraffe -Z auto.giraffe.gbz -m auto.min -d auto.dist -G - > /dev/null +rm: cannot remove 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 131: 3289491 Illegal instruction vg autoindex -p auto -w giraffe -g graphs/named_with_walk.gfa +t/52_vg_autoindex.t: line 134: 3289493 Illegal instruction vg giraffe -Z auto.giraffe.gbz -m auto.min -d auto.dist -f read.fq --named-coordinates > read.gam +rm: cannot remove 'auto.*': No such file or directory +t/52_vg_autoindex.t: line 140: 3289499 Illegal instruction vg autoindex -p auto -w giraffe -g graphs/named.gfa +t/52_vg_autoindex.t: line 143: 3289501 Illegal instruction vg giraffe -Z auto.giraffe.gbz -m auto.min -d auto.dist -f read.fq --named-coordinates > read.gam rm: cannot remove 'auto.*': No such file or directory -[vg autoindex] Executing command: vg autoindex -p auto -w map -r tiny/tiny.fa -v tiny/tiny.vcf.gz --force-unphased -[IndexRegistry]: Chunking inputs for parallelism. -[IndexRegistry]: Constructing VG graph from FASTA and VCF input. -[IndexRegistry]: Constructing XG graph from VG graph. -[IndexRegistry]: Pruning complex regions of VG to prepare for GCSA indexing. -[IndexRegistry]: Constructing GCSA/LCP indexes. -[vg autoindex] Executing command: vg autoindex -p auto -w map -r small/x.fa -v small/x.vcf.gz -r small/y.fa -v small/y.vcf.gz -[IndexRegistry]: Checking for phasing in VCF(s). -[IndexRegistry]: Chunking inputs for parallelism. -index file small/y.fa.fai not found, generating... -[IndexRegistry]: Constructing VG graph from FASTA and VCF input. -[IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. -[IndexRegistry]: Merging contig GBWTs. -[IndexRegistry]: Stripping allele paths from VG. -[IndexRegistry]: Constructing XG graph from VG graph. -[IndexRegistry]: Pruning complex regions of VG to prepare for GCSA indexing with GBWT unfolding. -[IndexRegistry]: Constructing GCSA/LCP indexes. -[vg autoindex] Executing command: vg autoindex -p auto -w map -r small/xy.fa -v small/xy2.vcf.gz -[IndexRegistry]: Checking for phasing in VCF(s). -[IndexRegistry]: Chunking inputs for parallelism. -[IndexRegistry]: Chunking FASTA(s). -[IndexRegistry]: Chunking VCF(s). -[IndexRegistry]: Constructing VG graph from FASTA and VCF input. -[IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. -[IndexRegistry]: Merging contig GBWTs. -[IndexRegistry]: Stripping allele paths from VG. -[IndexRegistry]: Constructing XG graph from VG graph. -[IndexRegistry]: Pruning complex regions of VG to prepare for GCSA indexing with GBWT unfolding. -[IndexRegistry]: Constructing GCSA/LCP indexes. -[vg autoindex] Executing command: vg autoindex -p auto -w mpmap -w rpvg -r tiny/tiny.fa -v tiny/tiny.vcf.gz -x tiny/tiny.gtf -[IndexRegistry]: Checking for phasing in VCF(s). -[IndexRegistry]: Chunking inputs for parallelism. -[IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. -[IndexRegistry]: Constructing GBWT from spliced VG graph and phased VCF input. -[IndexRegistry]: Stripping allele paths from spliced VG. -[IndexRegistry]: Constructing haplotype-transcript GBWT and finishing spliced VG. -[IndexRegistry]: Joining transcript origin table. -[IndexRegistry]: Constructing spliced XG graph from spliced VG graph. -[IndexRegistry]: Constructing distance index for a spliced graph. -[IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing with GBWT unfolding. -[IndexRegistry]: Constructing GCSA/LCP indexes. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - -[vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Identifying reference paths -[vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist -[vg mpmap] elapsed time 0 s: Completed loading distance index -[vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. -[vg autoindex] Executing command: vg autoindex -p auto -w mpmap -r tiny/tiny.fa -v tiny/tiny.vcf.gz -x tiny/tiny.gtf --force-unphased -[IndexRegistry]: Chunking inputs for parallelism. -[IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. -[IndexRegistry]: Finishing spliced VG. -[IndexRegistry]: Constructing spliced XG graph from spliced VG graph. -[IndexRegistry]: Constructing distance index for a spliced graph. -[IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. -[IndexRegistry]: Constructing GCSA/LCP indexes. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - -[vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Identifying reference paths -[vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist -[vg mpmap] elapsed time 0 s: Completed loading distance index -[vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. -[vg autoindex] Executing command: vg autoindex -p auto -w mpmap -r tiny/tiny.fa -x tiny/tiny.gtf -[IndexRegistry]: Chunking inputs for parallelism. -[IndexRegistry]: Constructing spliced VG graph from FASTA input. -[IndexRegistry]: Finishing spliced VG. -[IndexRegistry]: Constructing spliced XG graph from spliced VG graph. -[IndexRegistry]: Constructing distance index for a spliced graph. -[IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. -[IndexRegistry]: Constructing GCSA/LCP indexes. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - -[vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Identifying reference paths -[vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist -[vg mpmap] elapsed time 0 s: Completed loading distance index -[vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. -[vg autoindex] Executing command: vg autoindex -p auto -w mpmap -w rpvg -r small/x.fa -r small/y.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/x.gtf -x small/y.gtf -[IndexRegistry]: Checking for phasing in VCF(s). -[IndexRegistry]: Chunking inputs for parallelism. -[IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. -[IndexRegistry]: Constructing GBWT from spliced VG graph and phased VCF input. -[IndexRegistry]: Merging contig GBWTs. -[IndexRegistry]: Stripping allele paths from spliced VG. -[IndexRegistry]: Constructing haplotype-transcript GBWT and finishing spliced VG. -[IndexRegistry]: Merging contig GBWTs. -[IndexRegistry]: Joining transcript origin table. -[IndexRegistry]: Constructing spliced XG graph from spliced VG graph. -[IndexRegistry]: Constructing distance index for a spliced graph. -[IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing with GBWT unfolding. -[IndexRegistry]: Constructing GCSA/LCP indexes. -[vg autoindex] Executing command: vg autoindex -p auto -w mpmap -r small/x.fa -r small/y.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/x.gtf -x small/y.gtf --force-unphased -[IndexRegistry]: Chunking inputs for parallelism. -[IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. -[IndexRegistry]: Finishing spliced VG. -[IndexRegistry]: Constructing spliced XG graph from spliced VG graph. -[IndexRegistry]: Constructing distance index for a spliced graph. -[IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. -[IndexRegistry]: Constructing GCSA/LCP indexes. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - -[vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Identifying reference paths -[vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist -[vg mpmap] elapsed time 0 s: Completed loading distance index -[vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. -[vg autoindex] Executing command: vg autoindex -p auto -w mpmap -w rpvg -r small/x.fa -r small/y.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/xy.gtf -[IndexRegistry]: Checking for phasing in VCF(s). -[IndexRegistry]: Chunking inputs for parallelism. -[IndexRegistry]: Chunking FASTA(s). -[IndexRegistry]: Chunking VCF(s). -[IndexRegistry]: Chunking GTF/GFF(s). -[IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. -[IndexRegistry]: Constructing GBWT from spliced VG graph and phased VCF input. -[IndexRegistry]: Merging contig GBWTs. -[IndexRegistry]: Stripping allele paths from spliced VG. -[IndexRegistry]: Constructing haplotype-transcript GBWT and finishing spliced VG. -[IndexRegistry]: Merging contig GBWTs. -[IndexRegistry]: Joining transcript origin table. -[IndexRegistry]: Constructing spliced XG graph from spliced VG graph. -[IndexRegistry]: Constructing distance index for a spliced graph. -[IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing with GBWT unfolding. -[IndexRegistry]: Constructing GCSA/LCP indexes. -[vg autoindex] Executing command: vg autoindex -p auto -w mpmap -w rpvg -r small/xy.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/xy.gtf -[IndexRegistry]: Checking for phasing in VCF(s). -[IndexRegistry]: Chunking inputs for parallelism. -[IndexRegistry]: Chunking FASTA(s). -[IndexRegistry]: Chunking VCF(s). -[IndexRegistry]: Chunking GTF/GFF(s). -[IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. -[IndexRegistry]: Constructing GBWT from spliced VG graph and phased VCF input. -[IndexRegistry]: Merging contig GBWTs. -[IndexRegistry]: Stripping allele paths from spliced VG. -[IndexRegistry]: Constructing haplotype-transcript GBWT and finishing spliced VG. -[IndexRegistry]: Merging contig GBWTs. -[IndexRegistry]: Joining transcript origin table. -[IndexRegistry]: Constructing spliced XG graph from spliced VG graph. -[IndexRegistry]: Constructing distance index for a spliced graph. -[IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing with GBWT unfolding. -[IndexRegistry]: Constructing GCSA/LCP indexes. -[vg autoindex] Executing command: vg autoindex -p auto -w mpmap -g graphs/gfa_with_w_lines.gfa -x graphs/gfa_with_w_lines.gtf -[IndexRegistry]: Checking for haplotype lines in GFA. -[IndexRegistry]: Constructing a GBZ from GFA input. -[IndexRegistry]: Adding splice junctions to GBZ-format graph. -[IndexRegistry]: Constructing spliced XG graph from spliced VG graph. -[IndexRegistry]: Constructing distance index for a spliced graph. -[IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. -[IndexRegistry]: Constructing GCSA/LCP indexes. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - -[vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Identifying reference paths -[vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist -[vg mpmap] elapsed time 0 s: Completed loading distance index -[vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. -[vg autoindex] Executing command: vg autoindex -p auto -w mpmap -g graphs/gfa_with_w_lines.gfa -x graphs/gfa_with_w_lines.gtf -H graphs/gfa_with_w_lines_haplo.gtf -[IndexRegistry]: Checking for haplotype lines in GFA. -[IndexRegistry]: Constructing a GBZ from GFA input. -[IndexRegistry]: Adding splice junctions to GBZ-format graph. -[IndexRegistry]: Constructing spliced XG graph from spliced VG graph. -[IndexRegistry]: Constructing distance index for a spliced graph. -[IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. -[IndexRegistry]: Constructing GCSA/LCP indexes. -[vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - -[vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg -[vg mpmap] elapsed time 0 s: Completed loading graph -[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. -[vg mpmap] elapsed time 0 s: Identifying reference paths -[vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist -[vg mpmap] elapsed time 0 s: Completed loading distance index -[vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa -[vg mpmap] elapsed time 0 s: Completed loading GCSA2 -[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries -[vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp -[vg mpmap] elapsed time 0 s: Completed loading LCP -[vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread -[vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. -[vg autoindex] Executing command: vg autoindex -p auto -w rpvg -w mpmap -g graphs/gfa_with_w_lines.gfa -x graphs/gfa_with_w_lines.gtf -[IndexRegistry]: Checking for haplotype lines in GFA. -[IndexRegistry]: Constructing a GBZ from GFA input. -[IndexRegistry]: Constructing haplotype-transcript GBWT and spliced graph from GBZ-format graph. -[IndexRegistry]: Joining transcript origin table. -[IndexRegistry]: Constructing spliced XG graph from spliced VG graph. -[IndexRegistry]: Constructing distance index for a spliced graph. -[IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. -[IndexRegistry]: Constructing GCSA/LCP indexes. -[vg autoindex] Executing command: vg autoindex -p auto -w rpvg -w mpmap -g graphs/gfa_with_w_lines.gfa -x graphs/gfa_with_w_lines.gtf -H graphs/gfa_with_w_lines_haplo.gtf -[IndexRegistry]: Checking for haplotype lines in GFA. -[IndexRegistry]: Constructing a GBZ from GFA input. -[IndexRegistry]: Constructing haplotype-transcript GBWT and spliced graph from GBZ-format graph. -[IndexRegistry]: Joining transcript origin table. -[IndexRegistry]: Constructing spliced XG graph from spliced VG graph. -[IndexRegistry]: Constructing distance index for a spliced graph. -[IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. -[IndexRegistry]: Constructing GCSA/LCP indexes. -[vg autoindex] Executing command: vg autoindex -p auto -w giraffe -r tiny/tiny.fa -v tiny/tiny.vcf.gz -[IndexRegistry]: Checking for phasing in VCF(s). -[IndexRegistry]: Chunking inputs for parallelism. -[IndexRegistry]: Constructing VG graph from FASTA and VCF input. -[IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. -[IndexRegistry]: Stripping allele paths from VG. -[IndexRegistry]: Constructing XG graph from VG graph. -[IndexRegistry]: Downsampling full GBWT. -[IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. -[IndexRegistry]: Constructing GBZ. -[IndexRegistry]: Constructing distance index for Giraffe. -[IndexRegistry]: Constructing minimizer index. -[vg autoindex] Executing command: vg autoindex -p auto -w giraffe -g graphs/gfa_with_w_lines.gfa -[IndexRegistry]: Checking for haplotype lines in GFA. -[IndexRegistry]: Constructing a GBZ from GFA input. -[IndexRegistry]: Constructing distance index for Giraffe. -[IndexRegistry]: Constructing minimizer index. -warning [vg convert]: currently cannot convert GFA directly to XG; converting through another format -[vg autoindex] Executing command: vg autoindex -p auto -w giraffe -g graphs/named_with_walk.gfa -[IndexRegistry]: Checking for haplotype lines in GFA. -[IndexRegistry]: Constructing a GBZ from GFA input. -[IndexRegistry]: Constructing distance index for Giraffe. -[IndexRegistry]: Constructing minimizer index. -[vg autoindex] Executing command: vg autoindex -p auto -w giraffe -g graphs/named.gfa -[IndexRegistry]: Checking for haplotype lines in GFA. -[IndexRegistry]: Constructing VG graph from GFA input. -[IndexRegistry]: Constructing XG graph from VG graph. -[IndexRegistry]: Constructing a greedy path cover GBWT -[IndexRegistry]: Constructing GBZ using NamedNodeBackTranslation. -[IndexRegistry]: Constructing distance index for Giraffe. -[IndexRegistry]: Constructing minimizer index. t/52_vg_autoindex.t ... 1..49 -ok 1 - autoindexing successfully completes indexing for vg map with basic input -ok 2 - autoindexing makes 3 outputs for vg map -ok 3 - autoindexing makes an XG for vg map -ok 4 - autoindexing makes a GCSA2/LCP pair for vg map -ok 5 - basic autoindexing results can be used by vg map -ok 6 - autoindexing successfully completes indexing for vg map with chunked input -ok 7 - chunked autoindexing results can be used by vg map -ok 8 - autoindexing successfully completes indexing for vg map with phased input -ok 9 - phased autoindexing results can be used by vg map -ok 10 - autoindexing successfully completes indexing for vg mpmap with unchunked input -ok 11 - autoindexing creates 6 files for mpmap/rpvg -ok 12 - basic autoindexing results can be used by vg mpmap -ok 13 - haplotype transcript GBWT made by autoindex is valid -ok 14 - transcript origin table has expected number of rows -ok 15 - autoindexing successfully completes indexing for vg mpmap with unchunked, unphased input -ok 16 - autoindexing creates 4 files for mpmap/rpvg -ok 17 - basic unphased autoindexing results can be used by vg mpmap -ok 18 - autoindexing successfully completes indexing for vg mpmap without variants -ok 19 - autoindexing creates 4 files for mpmap without variants -ok 20 - autoindexing results with no variants can be used by vg mpmap -ok 21 - autoindexing successfully completes indexing for vg mpmap with chunked input -ok 22 - autoindexing creates 6 files for mpmap/rpvg with chunked input -ok 23 - autoindexing successfully completes indexing for vg mpmap with unphased chunked input -ok 24 - autoindexing creates 4 files for mpmap/rpvg with chunked input -ok 25 - autoindexing results with chunked unphased input can be used by vg mpmap -ok 26 - autoindexing successfully completes indexing for vg mpmap with partially chunked input -ok 27 - autoindexing successfully completes indexing for vg mpmap with another partially chunked input -ok 28 - autoindexing successfully completes indexing for vg mpmap with GFA input -ok 29 - autoindexing results with GFA input can be used by vg mpmap -ok 30 - autoindexing successfully completes indexing for vg mpmap with GFA input and a haplotype GTF -ok 31 - autoindexing results with GFA input and a haplotype GTF can be used by vg mpmap -ok 32 - autoindexing successfully completes indexing for vg mpmap and rpvg with GFA input -ok 33 - autoindexing successfully completes indexing for vg mpmap and rpvg with GFA input and a haplotype GTF -ok 34 - autoindexing successfully completes indexing for vg giraffe with unchunked input -ok 35 - autoindexing creates 3 inputs for vg giraffe -ok 36 - basic autoindexing results can be used by vg giraffe -ok 37 - autoindexing successfully completes indexing for vg giraffe with GFA input with W-lines -ok 38 - autoindexing creates 3 inputs for vg giraffe from GFA input -ok 39 - GFA autoindexing results can be used by vg giraffe -ok 40 - autoindexing successfully completes on a GFA with named segments and W-lines -ok 41 - GFA segment names are available in output GAM when a walk exists -ok 42 - autoindexing successfully completes on a GFA with named segments and no W-lines -ok 43 - GFA segment names are available in output GAM when no walks exist -ok 44 - Running out of room during k-mer enumeration triggers a rewind +not ok 1 - autoindexing successfully completes indexing for vg map with basic input +# got: '132' +# expected: '0' +not ok 2 - autoindexing makes 3 outputs for vg map +# got: '0' +# expected: '3' +not ok 3 - autoindexing makes an XG for vg map +# got: '0' +# expected: '1' +not ok 4 - autoindexing makes a GCSA2/LCP pair for vg map +# got: '0' +# expected: '2' +not ok 5 - basic autoindexing results can be used by vg map +# got: '132' +# expected: '0' +not ok 6 - autoindexing successfully completes indexing for vg map with chunked input +# got: '132' +# expected: '0' +not ok 7 - chunked autoindexing results can be used by vg map +# got: '132' +# expected: '0' +not ok 8 - autoindexing successfully completes indexing for vg map with phased input +# got: '132' +# expected: '0' +not ok 9 - phased autoindexing results can be used by vg map +# got: '132' +# expected: '0' +not ok 10 - autoindexing successfully completes indexing for vg mpmap with unchunked input +# got: '132' +# expected: '0' +not ok 11 - autoindexing creates 6 files for mpmap/rpvg +# got: '0' +# expected: '6' +not ok 12 - basic autoindexing results can be used by vg mpmap +# got: '132' +# expected: '0' +not ok 13 - haplotype transcript GBWT made by autoindex is valid +# got: '0' +# expected: '6' +not ok 14 - transcript origin table has expected number of rows +# got: '0' +# expected: '7' +not ok 15 - autoindexing successfully completes indexing for vg mpmap with unchunked, unphased input +# got: '132' +# expected: '0' +not ok 16 - autoindexing creates 4 files for mpmap/rpvg +# got: '0' +# expected: '4' +not ok 17 - basic unphased autoindexing results can be used by vg mpmap +# got: '132' +# expected: '0' +not ok 18 - autoindexing successfully completes indexing for vg mpmap without variants +# got: '132' +# expected: '0' +not ok 19 - autoindexing creates 4 files for mpmap without variants +# got: '0' +# expected: '4' +not ok 20 - autoindexing results with no variants can be used by vg mpmap +# got: '132' +# expected: '0' +not ok 21 - autoindexing successfully completes indexing for vg mpmap with chunked input +# got: '132' +# expected: '0' +not ok 22 - autoindexing creates 6 files for mpmap/rpvg with chunked input +# got: '0' +# expected: '6' +not ok 23 - autoindexing successfully completes indexing for vg mpmap with unphased chunked input +# got: '132' +# expected: '0' +not ok 24 - autoindexing creates 4 files for mpmap/rpvg with chunked input +# got: '0' +# expected: '4' +not ok 25 - autoindexing results with chunked unphased input can be used by vg mpmap +# got: '132' +# expected: '0' +not ok 26 - autoindexing successfully completes indexing for vg mpmap with partially chunked input +# got: '132' +# expected: '0' +not ok 27 - autoindexing successfully completes indexing for vg mpmap with another partially chunked input +# got: '132' +# expected: '0' +not ok 28 - autoindexing successfully completes indexing for vg mpmap with GFA input +# got: '132' +# expected: '0' +not ok 29 - autoindexing results with GFA input can be used by vg mpmap +# got: '132' +# expected: '0' +not ok 30 - autoindexing successfully completes indexing for vg mpmap with GFA input and a haplotype GTF +# got: '132' +# expected: '0' +not ok 31 - autoindexing results with GFA input and a haplotype GTF can be used by vg mpmap +# got: '132' +# expected: '0' +not ok 32 - autoindexing successfully completes indexing for vg mpmap and rpvg with GFA input +# got: '132' +# expected: '0' +not ok 33 - autoindexing successfully completes indexing for vg mpmap and rpvg with GFA input and a haplotype GTF +# got: '132' +# expected: '0' +not ok 34 - autoindexing successfully completes indexing for vg giraffe with unchunked input +# got: '132' +# expected: '0' +not ok 35 - autoindexing creates 3 inputs for vg giraffe +# got: '0' +# expected: '3' +not ok 36 - basic autoindexing results can be used by vg giraffe +# got: '132' +# expected: '0' +not ok 37 - autoindexing successfully completes indexing for vg giraffe with GFA input with W-lines +# got: '132' +# expected: '0' +not ok 38 - autoindexing creates 3 inputs for vg giraffe from GFA input +# got: '0' +# expected: '3' +not ok 39 - GFA autoindexing results can be used by vg giraffe +# got: '132' +# expected: '0' +not ok 40 - autoindexing successfully completes on a GFA with named segments and W-lines +# got: '132' +# expected: '0' +not ok 41 - GFA segment names are available in output GAM when a walk exists +# got: '' +# expected: 'Ishmael' +not ok 42 - autoindexing successfully completes on a GFA with named segments and no W-lines +# got: '132' +# expected: '0' +not ok 43 - GFA segment names are available in output GAM when no walks exist +# got: '' +# expected: 'Ishmael' +not ok 44 - Running out of room during k-mer enumeration triggers a rewind +# got: '0' +# expected: '1' ok 45 - Indexing is successful after rewinding from k-mer generation -ok 46 - Running out of room during GCSA2 indexing triggers a rewind +not ok 46 - Running out of room during GCSA2 indexing triggers a rewind +# got: '0' +# expected: '1' ok 47 - Indexing is successful after rewinding from GCSA2 indexing -ok 48 - Running out of memory during GCSA2 indexing triggers a rewind +not ok 48 - Running out of memory during GCSA2 indexing triggers a rewind +# got: '0' +# expected: '1' ok 49 - Indexing is successful after rewinding from GCSA2 indexing -ok - -WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. - -!!! -WARNING -!!! -vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. - -warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. -[algorithms::normalize] iteration 1 current length 1014 -[algorithms::normalize] normalized in 0 steps -graph: valid -graph: valid -graph: valid -graph: valid -graph: valid -graph: valid +Failed 46/49 subtests +t/53_clip.t: line 10: 3289523 Illegal instruction vg msga -f GRCh38_alts/FASTA/HLA/V-352962.fa -t 1 -k 16 + 3289524 | vg mod -U 10 - + 3289525 | vg mod -c - > hla.vg +t/53_clip.t: line 14: 3289526 Illegal instruction vg clip hla.vg -b region.bed > clip_flat.vg +t/53_clip.t: line 15: 3289527 Illegal instruction vg validate clip_flat.vg +t/53_clip.t: line 27: 3289545 Illegal instruction vg clip hla.vg -b region.bed > clip.vg +t/53_clip.t: line 28: 3289546 Illegal instruction vg validate clip.vg +t/53_clip.t: line 36: 3289552 Illegal instruction vg clip hla.vg -b region.bed > clip.vg +t/53_clip.t: line 37: 3289553 Illegal instruction vg validate clip.vg +t/53_clip.t: line 44: 3289559 Illegal instruction vg clip hla.vg -d 4 -P "gi|568815551:1054737-1055734" > clip.vg +t/53_clip.t: line 45: 3289560 Illegal instruction vg validate clip.vg +t/53_clip.t: line 53: 3289566 Illegal instruction vg clip hla.vg -b region.bed -d 4 > clip.vg +t/53_clip.t: line 54: 3289567 Illegal instruction vg validate clip.vg +t/53_clip.t: line 65: 3289574 Illegal instruction vg clip hla.vg -b region.bed -d 4 > clip.vg +t/53_clip.t: line 66: 3289575 Illegal instruction vg validate clip.vg t/53_clip.t ........... 1..17 -ok 1 - clipped graph is valid +not ok 1 - clipped graph is valid +# got: '132' +# expected: '0' ok 2 - every step in clipped graph belongs to reference path -ok 3 - clipped graph has same length as ref path -ok 4 - clipped graph is valid -ok 5 - Just one node filtered -ok 6 - clipped graph is valid -ok 7 - Just one edge filtered -ok 8 - clipped graph is valid -ok 9 - Just one node filtered -ok 10 - clipped graph is valid +not ok 3 - unnamed test +# got: 'clipped graph has same length as ref path' +# expected: '' +not ok 4 - clipped graph is valid +# got: '132' +# expected: '0' +not ok 5 - Just one node filtered +# got: '0' +# expected: '49' +not ok 6 - clipped graph is valid +# got: '132' +# expected: '0' +not ok 7 - Just one edge filtered +# got: '0' +# expected: '65' +not ok 8 - clipped graph is valid +# got: '132' +# expected: '0' +not ok 9 - Just one node filtered +# got: '0' +# expected: '49' +not ok 10 - clipped graph is valid +# got: '132' +# expected: '0' ok 11 - clipping bad region changes nothing -ok 12 - clipped graph is valid -ok 13 - Just one node filtered +not ok 12 - clipped graph is valid +# got: '132' +# expected: '0' +not ok 13 - Just one node filtered +# got: '0' +# expected: '49' ok 14 - stub clipping removed all stubs -ok 15 - region clipping filtered out only 2 / 4 stub nodes -ok 16 - Correct head after path stubbification -ok 17 - Correct tail after path stubbification -ok +not ok 15 - unnamed test +# got: '17' +# expected: 'region clipping filtered out only 2 / 4 stub nodes' +not ok 16 - unnamed test +# got: '1' +# expected: 'Correct head after path stubbification' +not ok 17 - unnamed test +# got: '15' +# expected: 'Correct tail after path stubbification' +Failed 14/17 subtests +t/54_vg_haplotypes.t: line 16: 3289606 Illegal instruction vg gbwt -G haplotype-sampling/micb-kir3dl1.gfa --gbz-format -g full.gbz -r full.ri +t/54_vg_haplotypes.t: line 17: 3289607 Illegal instruction vg index -j full.dist full.gbz +t/54_vg_haplotypes.t: line 20: 3289608 Illegal instruction vg haplotypes --validate --subchain-length 300 -H full.hapl full.gbz +t/54_vg_haplotypes.t: line 22: 3289609 Illegal instruction vg haplotypes --validate -i full.hapl -k haplotype-sampling/HG003.kff --include-reference -g indirect.gbz full.gbz +t/54_vg_haplotypes.t: line 29: 3289613 Illegal instruction vg haplotypes --validate --subchain-length 300 -k haplotype-sampling/HG003.kff --include-reference -g direct.gbz full.gbz +cmp: indirect.gbz: No such file or directory +t/54_vg_haplotypes.t: line 35: 3289615 Illegal instruction vg haplotypes --validate -i full.hapl -k haplotype-sampling/HG003.kff -g no_ref.gbz full.gbz +t/54_vg_haplotypes.t: line 42: 3289619 Illegal instruction vg haplotypes --validate -i full.hapl -k haplotype-sampling/HG003.kff --include-reference --diploid-sampling -g diploid.gbz full.gbz +t/54_vg_haplotypes.t: line 49: 3289623 Illegal instruction vg haplotypes -i full.hapl -k haplotype-sampling/HG003.kff --preset diploid -g diploid2.gbz full.gbz +cmp: diploid.gbz: No such file or directory +t/54_vg_haplotypes.t: line 56: 3289625 Illegal instruction vg giraffe -Z full.gbz --haplotype-name full.hapl --kff-name haplotype-sampling/HG003.kff -f haplotype-sampling/HG003.fq.gz > default.gam 2> /dev/null +cmp: diploid.gbz: No such file or directory +t/54_vg_haplotypes.t: line 64: 3289627 Illegal instruction vg giraffe -Z full.gbz --haplotype-name full.hapl --kff-name haplotype-sampling/HG003.kff --index-basename sampled -N 003HG -f haplotype-sampling/HG003.fq.gz > specified.gam 2> /dev/null +cmp: full.HG003.gbz: No such file or directory +rm: cannot remove 'full.gbz': No such file or directory +rm: cannot remove 'full.ri': No such file or directory +rm: cannot remove 'full.dist': No such file or directory +rm: cannot remove 'full.hapl': No such file or directory t/54_vg_haplotypes.t .. 1..21 -ok 1 - generating haplotype information -ok 2 - sampling from existing haplotype information -ok 3 - 1 generated + 2 reference samples -ok 4 - 2 contigs -ok 5 - 4 generated + 2 reference haplotypes -ok 6 - sampling the haplotypes directly -ok 7 - the outputs are identical -ok 8 - sampling without adding reference -ok 9 - 1 sample -ok 10 - 2 contigs -ok 11 - 4 haplotypes -ok 12 - diploid sampling -ok 13 - 1 generated + 2 reference samples -ok 14 - 2 contigs -ok 15 - 2 generated + 2 reference haplotypes -ok 16 - diploid sampling using a preset -ok 17 - the outputs are identical -ok 18 - Giraffe integration with a guessed output name -ok 19 - the sampled graph is identical to a manually sampled one -ok 20 - Giraffe integration with a specified output name -ok 21 - the sampled graphs are identical -ok +not ok 1 - generating haplotype information +# got: '132' +# expected: '0' +not ok 2 - sampling from existing haplotype information +# got: '132' +# expected: '0' +not ok 3 - unnamed test +# got: '3' +# expected: '1 generated + 2 reference samples' +not ok 4 - unnamed test +# got: '2' +# expected: '2 contigs' +not ok 5 - unnamed test +# got: '6' +# expected: '4 generated + 2 reference haplotypes' +not ok 6 - sampling the haplotypes directly +# got: '132' +# expected: '0' +not ok 7 - the outputs are identical +# got: '2' +# expected: '0' +not ok 8 - sampling without adding reference +# got: '132' +# expected: '0' +not ok 9 - unnamed test +# got: '1' +# expected: '1 sample' +not ok 10 - unnamed test +# got: '2' +# expected: '2 contigs' +not ok 11 - unnamed test +# got: '4' +# expected: '4 haplotypes' +not ok 12 - diploid sampling +# got: '132' +# expected: '0' +not ok 13 - unnamed test +# got: '3' +# expected: '1 generated + 2 reference samples' +not ok 14 - unnamed test +# got: '2' +# expected: '2 contigs' +not ok 15 - unnamed test +# got: '4' +# expected: '2 generated + 2 reference haplotypes' +not ok 16 - diploid sampling using a preset +# got: '132' +# expected: '0' +not ok 17 - the outputs are identical +# got: '2' +# expected: '0' +not ok 18 - Giraffe integration with a guessed output name +# got: '132' +# expected: '0' +not ok 19 - the sampled graph is identical to a manually sampled one +# got: '2' +# expected: '0' +not ok 20 - Giraffe integration with a specified output name +# got: '132' +# expected: '0' +not ok 21 - the sampled graphs are identical +# got: '2' +# expected: '0' +Failed 21/21 subtests Test Summary Report ------------------- -t/02_vg_construct.t (Wstat: 0 Tests: 30 Failed: 1) - Failed test: 7 -t/50_vg_giraffe.t (Wstat: 0 Tests: 50 Failed: 3) - Failed tests: 48-50 -Files=53, Tests=1138, 1018 wallclock secs ( 0.56 usr 0.13 sys + 6099.17 cusr 1025.03 csys = 7124.89 CPU) +t/00_unittest.t (Wstat: 0 Tests: 1 Failed: 1) + Failed test: 1 +t/02_vg_construct.t (Wstat: 0 Tests: 30 Failed: 24) + Failed tests: 1-7, 9-11, 13, 17-22, 24-30 +t/03_vg_view.t (Wstat: 0 Tests: 23 Failed: 15) + Failed tests: 1-4, 6, 11-15, 17-20, 23 +t/04_vg_align.t (Wstat: 0 Tests: 20 Failed: 20) + Failed tests: 1-20 +t/05_vg_find.t (Wstat: 0 Tests: 29 Failed: 25) + Failed tests: 1-14, 16-21, 23-24, 26-27, 29 +t/06_vg_index.t (Wstat: 0 Tests: 54 Failed: 50) + Failed tests: 1-10, 12-16, 18-21, 23-36, 38-54 +t/07_vg_map.t (Wstat: 0 Tests: 55 Failed: 50) + Failed tests: 1-14, 17-22, 25-32, 34-55 +t/08_vg_ids.t (Wstat: 0 Tests: 10 Failed: 9) + Failed tests: 1-5, 7-10 +t/09_vg_concat.t (Wstat: 0 Tests: 4 Failed: 2) + Failed tests: 2, 4 +t/10_vg_stats.t (Wstat: 0 Tests: 21 Failed: 20) + Failed tests: 1-8, 10-21 +t/11_vg_paths.t (Wstat: 0 Tests: 20 Failed: 17) + Failed tests: 1-7, 9-14, 16-19 +t/12_vg_kmers.t (Wstat: 0 Tests: 10 Failed: 10) + Failed tests: 1-10 +t/13_vg_sim.t (Wstat: 0 Tests: 36 Failed: 31) + Failed tests: 1-5, 9-13, 15, 17-36 +t/14_vg_mod.t (Wstat: 0 Tests: 32 Failed: 25) + Failed tests: 2-11, 13-14, 16, 18-21, 24-25, 27-32 +t/15_vg_surject.t (Wstat: 256 (exited 1) Tests: 47 Failed: 42) + Failed tests: 1-15, 18-20, 22-35, 38-47 + Non-zero exit status: 1 +t/16_vg_msga.t (Wstat: 0 Tests: 14 Failed: 12) + Failed tests: 1-4, 7-14 +t/17_vg_augment.t (Wstat: 0 Tests: 39 Failed: 31) + Failed tests: 1-19, 22-23, 26-27, 29-30, 32-33, 35-36 + 38-39 +t/18_vg_call.t (Wstat: 0 Tests: 19 Failed: 6) + Failed tests: 2, 11, 14-15, 17-18 +t/20_vgtordf.t (Wstat: 0 Tests: 6 Failed: 4) + Failed tests: 1-2, 5-6 +t/21_vg_filter.t (Wstat: 0 Tests: 13 Failed: 5) + Failed tests: 1-2, 5, 9, 12 +t/25_circularize.t (Wstat: 0 Tests: 2 Failed: 2) + Failed tests: 1-2 +t/26_deconstruct.t (Wstat: 0 Tests: 37 Failed: 30) + Failed tests: 1-4, 6-10, 12-17, 23-37 +t/27_vg_genotype.t (Wstat: 0 Tests: 5 Failed: 4) + Failed tests: 1-2, 4-5 +t/28_translate.t (Wstat: 0 Tests: 2 Failed: 1) + Failed test: 2 +t/30_vg_chunk.t (Wstat: 0 Tests: 32 Failed: 20) + Failed tests: 1-10, 12-18, 20-22 +t/31_vg_add.t (Wstat: 0 Tests: 12 Failed: 8) + Failed tests: 1-2, 4, 7-8, 10-12 +t/32_vg_snarls.t (Wstat: 0 Tests: 19 Failed: 14) + Failed tests: 1-5, 9, 11-18 +t/33_vg_mpmap.t (Wstat: 256 (exited 1) Tests: 21 Failed: 20) + Failed tests: 1-13, 15-21 + Non-zero exit status: 1 +t/34_vg_pack.t (Wstat: 0 Tests: 20 Failed: 9) + Failed tests: 1-4, 10-11, 18-20 +t/36_vg_annotate.t (Wstat: 0 Tests: 9 Failed: 7) + Failed tests: 1-2, 5-9 +t/37_vg_gbwt.t (Wstat: 0 Tests: 159 Failed: 158) + Failed tests: 1-23, 25-159 +t/38_vg_prune.t (Wstat: 0 Tests: 21 Failed: 21) + Failed tests: 1-21 +t/39_vg_inject.t (Wstat: 256 (exited 1) Tests: 14 Failed: 10) + Failed tests: 1-9, 13 + Non-zero exit status: 1 +t/40_vg_gamcompare.t (Wstat: 0 Tests: 7 Failed: 5) + Failed tests: 1-4, 7 +t/41_vg_viz.t (Wstat: 0 Tests: 4 Failed: 4) + Failed tests: 1-4 +t/42_vg_gamsort.t (Wstat: 0 Tests: 2 Failed: 1) + Failed test: 2 +t/43_vg_simplify.t (Wstat: 0 Tests: 5 Failed: 5) + Failed tests: 1-5 +t/44_vg_benchmark.t (Wstat: 0 Tests: 1 Failed: 1) + Failed test: 1 +t/45_vg_sort.t (Wstat: 0 Tests: 5 Failed: 5) + Failed tests: 1-5 +t/46_vg_minimizer.t (Wstat: 0 Tests: 16 Failed: 16) + Failed tests: 1-16 +t/47_vg_dotplot.t (Wstat: 0 Tests: 1 Failed: 1) + Failed test: 1 +t/48_vg_convert.t (Wstat: 0 Tests: 106 Failed: 47) + Failed tests: 20, 23, 30-32, 35-41, 43-48, 51, 54, 57 + 60-65, 67-68, 70-71, 73-80, 87-90, 93, 99 + 104, 106 +t/49_vg_depth.t (Wstat: 0 Tests: 6 Failed: 5) + Failed tests: 1-4, 6 +t/50_vg_giraffe.t (Wstat: 0 Tests: 50 Failed: 44) + Failed tests: 1-12, 14-15, 18, 20-44, 46, 48-50 +t/51_vg_combine.t (Wstat: 0 Tests: 10 Failed: 8) + Failed tests: 1-2, 4-5, 7-10 +t/52_vg_autoindex.t (Wstat: 0 Tests: 49 Failed: 46) + Failed tests: 1-44, 46, 48 +t/53_clip.t (Wstat: 0 Tests: 17 Failed: 14) + Failed tests: 1, 3-10, 12-13, 15-17 +t/54_vg_haplotypes.t (Wstat: 0 Tests: 21 Failed: 21) + Failed tests: 1-21 +Files=53, Tests=1138, 84 wallclock secs ( 0.73 usr 0.17 sys + 68.67 cusr 55.84 csys = 125.41 CPU) Result: FAIL Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Address sizes: 40 bits physical, 48 bits virtual Byte Order: Little Endian -CPU(s): 42 -On-line CPU(s) list: 0-41 -Vendor ID: GenuineIntel -Model name: Intel Core Processor (Haswell) -CPU family: 6 -Model: 60 -Thread(s) per core: 2 +CPU(s): 20 +On-line CPU(s) list: 0-19 +Vendor ID: AuthenticAMD +Model name: AMD Opteron 62xx class CPU +CPU family: 21 +Model: 1 +Thread(s) per core: 1 Core(s) per socket: 1 -Socket(s): 21 -Stepping: 1 -BogoMIPS: 4788.90 -Virtualization: VT-x +Socket(s): 20 +Stepping: 2 +BogoMIPS: 5199.99 +Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 syscall nx mmxext pdpe1gb rdtscp lm rep_good nopl cpuid extd_apicid tsc_known_freq pni pclmulqdq ssse3 cx16 sse4_1 sse4_2 x2apic popcnt aes xsave avx hypervisor lahf_lm cmp_legacy svm abm sse4a misalignsse 3dnowprefetch osvw ssbd ibpb vmmcall virt_ssbd arat npt nrip_save +Virtualization: AMD-V Hypervisor vendor: Microsoft Virtualization type: full -L1d cache: 672 KiB (21 instances) -L1i cache: 672 KiB (21 instances) -L2 cache: 84 MiB (21 instances) +L1d cache: 1.3 MiB (20 instances) +L1i cache: 1.3 MiB (20 instances) +L2 cache: 10 MiB (20 instances) NUMA node(s): 1 -NUMA node0 CPU(s): 0-41 +NUMA node0 CPU(s): 0-19 Vulnerability Gather data sampling: Not affected -Vulnerability Itlb multihit: KVM: Mitigation: VMX disabled -Vulnerability L1tf: Mitigation; PTE Inversion; VMX conditional cache flushes, SMT vulnerable -Vulnerability Mds: Mitigation; Clear CPU buffers; SMT Host state unknown -Vulnerability Meltdown: Mitigation; PTI -Vulnerability Mmio stale data: Unknown: No mitigations +Vulnerability Itlb multihit: Not affected +Vulnerability L1tf: Not affected +Vulnerability Mds: Not affected +Vulnerability Meltdown: Not affected +Vulnerability Mmio stale data: Not affected Vulnerability Reg file data sampling: Not affected -Vulnerability Retbleed: Not affected +Vulnerability Retbleed: Mitigation; untrained return thunk; SMT disabled Vulnerability Spec rstack overflow: Not affected Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl Vulnerability Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization -Vulnerability Spectre v2: Mitigation; Retpolines; IBPB conditional; IBRS_FW; STIBP conditional; RSB filling; PBRSB-eIBRS Not affected; BHI Retpoline -Vulnerability Srbds: Unknown: Dependent on hypervisor status -Vulnerability Tsx async abort: Mitigation; Clear CPU buffers; SMT Host state unknown +Vulnerability Spectre v2: Mitigation; Retpolines; IBPB conditional; STIBP disabled; RSB filling; PBRSB-eIBRS Not affected; BHI Not affected +Vulnerability Srbds: Not affected +Vulnerability Tsx async abort: Not affected make[1]: [debian/rules:75: override_dh_auto_test-arch] Error 255 (ignored) export BIN=/build/reproducible-path/vg-1.59.0+ds/debian/help/vg-plain \ ; echo "Testing ${BIN}" \ @@ -25286,81 +31539,81 @@ # got: '1' # expected: '0' Failed 25/29 subtests -t/06_vg_index.t: line 13: vg: command not found -t/06_vg_index.t: line 15: vg: command not found -t/06_vg_index.t: line 18: vg: command not found -t/06_vg_index.t: line 21: vg: command not found +t/06_vg_index.t: line 13: vg: käsku ei ole +t/06_vg_index.t: line 15: vg: käsku ei ole +t/06_vg_index.t: line 18: vg: käsku ei ole +t/06_vg_index.t: line 21: vg: käsku ei ole cmp: x.xg: No such file or directory -t/06_vg_index.t: line 27: vg: command not found +t/06_vg_index.t: line 27: vg: käsku ei ole cmp: x.gcsa: No such file or directory -t/06_vg_index.t: line 40: vg: command not found -t/06_vg_index.t: line 42: vg: command not found -t/06_vg_index.t: line 45: vg: command not found -t/06_vg_index.t: line 48: vg: command not found -t/06_vg_index.t: line 50: vg: command not found -t/06_vg_index.t: line 53: vg: command not found -t/06_vg_index.t: line 53: vg: command not found -t/06_vg_index.t: line 55: vg: command not found -t/06_vg_index.t: line 58: vg: command not found +t/06_vg_index.t: line 40: vg: käsku ei ole +t/06_vg_index.t: line 42: vg: käsku ei ole +t/06_vg_index.t: line 45: vg: käsku ei ole +t/06_vg_index.t: line 48: vg: käsku ei ole +t/06_vg_index.t: line 50: vg: käsku ei ole +t/06_vg_index.t: line 53: vg: käsku ei ole +t/06_vg_index.t: line 53: vg: käsku ei ole +t/06_vg_index.t: line 55: vg: käsku ei ole +t/06_vg_index.t: line 58: vg: käsku ei ole cmp: x.xg: No such file or directory -t/06_vg_index.t: line 64: vg: command not found +t/06_vg_index.t: line 64: vg: käsku ei ole cmp: x.gbwt: No such file or directory -t/06_vg_index.t: line 70: vg: command not found -t/06_vg_index.t: line 70: vg: command not found -t/06_vg_index.t: line 73: vg: command not found -t/06_vg_index.t: line 75: vg: command not found -t/06_vg_index.t: line 78: vg: command not found -t/06_vg_index.t: line 79: vg: command not found -t/06_vg_index.t: line 81: vg: command not found -t/06_vg_index.t: line 82: vg: command not found +t/06_vg_index.t: line 70: vg: käsku ei ole +t/06_vg_index.t: line 70: vg: käsku ei ole +t/06_vg_index.t: line 73: vg: käsku ei ole +t/06_vg_index.t: line 75: vg: käsku ei ole +t/06_vg_index.t: line 78: vg: käsku ei ole +t/06_vg_index.t: line 79: vg: käsku ei ole +t/06_vg_index.t: line 81: vg: käsku ei ole +t/06_vg_index.t: line 82: vg: käsku ei ole cmp: x-gaf.gbwt: No such file or directory -t/06_vg_index.t: line 95: vg: command not found -t/06_vg_index.t: line 108: vg: command not found -t/06_vg_index.t: line 110: vg: command not found -t/06_vg_index.t: line 113: vg: command not found -t/06_vg_index.t: line 116: vg: command not found +t/06_vg_index.t: line 95: vg: käsku ei ole +t/06_vg_index.t: line 108: vg: käsku ei ole +t/06_vg_index.t: line 110: vg: käsku ei ole +t/06_vg_index.t: line 113: vg: käsku ei ole +t/06_vg_index.t: line 116: vg: käsku ei ole cmp: xy.xg: No such file or directory -t/06_vg_index.t: line 130: vg: command not found -t/06_vg_index.t: line 132: vg: command not found -t/06_vg_index.t: line 135: vg: command not found -t/06_vg_index.t: line 138: vg: command not found -t/06_vg_index.t: line 141: vg: command not found -t/06_vg_index.t: line 144: vg: command not found -t/06_vg_index.t: line 147: vg: command not found +t/06_vg_index.t: line 130: vg: käsku ei ole +t/06_vg_index.t: line 132: vg: käsku ei ole +t/06_vg_index.t: line 135: vg: käsku ei ole +t/06_vg_index.t: line 138: vg: käsku ei ole +t/06_vg_index.t: line 141: vg: käsku ei ole +t/06_vg_index.t: line 144: vg: käsku ei ole +t/06_vg_index.t: line 147: vg: käsku ei ole cmp: xy.xg: No such file or directory -t/06_vg_index.t: line 163: vg: command not found -t/06_vg_index.t: line 173: vg: command not found -t/06_vg_index.t: line 177: vg: command not found -t/06_vg_index.t: line 178: vg: command not found -t/06_vg_index.t: line 182: vg: command not found -t/06_vg_index.t: line 183: vg: command not found -t/06_vg_index.t: line 183: vg: command not found -t/06_vg_index.t: line 186: vg: command not found -t/06_vg_index.t: line 187: vg: command not found +t/06_vg_index.t: line 163: vg: käsku ei ole +t/06_vg_index.t: line 173: vg: käsku ei ole +t/06_vg_index.t: line 177: vg: käsku ei ole +t/06_vg_index.t: line 178: vg: käsku ei ole +t/06_vg_index.t: line 182: vg: käsku ei ole +t/06_vg_index.t: line 183: vg: käsku ei ole +t/06_vg_index.t: line 183: vg: käsku ei ole +t/06_vg_index.t: line 186: vg: käsku ei ole +t/06_vg_index.t: line 187: vg: käsku ei ole t/06_vg_index.t: line 189: x1337.sorted.gam.gai: No such file or directory t/06_vg_index.t: line 189: x1337.sorted.gam.gai2: No such file or directory -t/06_vg_index.t: line 194: vg: command not found -t/06_vg_index.t: line 195: vg: command not found -t/06_vg_index.t: line 196: vg: command not found -t/06_vg_index.t: line 198: vg: command not found -t/06_vg_index.t: line 200: vg: command not found -t/06_vg_index.t: line 208: vg: command not found -t/06_vg_index.t: line 211: vg: command not found -t/06_vg_index.t: line 217: vg: command not found -t/06_vg_index.t: line 227: vg: command not found -t/06_vg_index.t: line 229: vg: command not found -t/06_vg_index.t: line 233: vg: command not found -t/06_vg_index.t: line 246: vg: command not found -t/06_vg_index.t: line 248: vg: command not found -t/06_vg_index.t: line 251: vg: command not found -t/06_vg_index.t: line 254: vg: command not found -t/06_vg_index.t: line 254: vg: command not found -t/06_vg_index.t: line 257: vg: command not found -t/06_vg_index.t: line 257: vg: command not found -t/06_vg_index.t: line 263: vg: command not found -t/06_vg_index.t: line 264: vg: command not found -t/06_vg_index.t: line 265: vg: command not found -t/06_vg_index.t: line 268: vg: command not found +t/06_vg_index.t: line 194: vg: käsku ei ole +t/06_vg_index.t: line 195: vg: käsku ei ole +t/06_vg_index.t: line 196: vg: käsku ei ole +t/06_vg_index.t: line 198: vg: käsku ei ole +t/06_vg_index.t: line 200: vg: käsku ei ole +t/06_vg_index.t: line 208: vg: käsku ei ole +t/06_vg_index.t: line 211: vg: käsku ei ole +t/06_vg_index.t: line 217: vg: käsku ei ole +t/06_vg_index.t: line 227: vg: käsku ei ole +t/06_vg_index.t: line 229: vg: käsku ei ole +t/06_vg_index.t: line 233: vg: käsku ei ole +t/06_vg_index.t: line 246: vg: käsku ei ole +t/06_vg_index.t: line 248: vg: käsku ei ole +t/06_vg_index.t: line 251: vg: käsku ei ole +t/06_vg_index.t: line 254: vg: käsku ei ole +t/06_vg_index.t: line 254: vg: käsku ei ole +t/06_vg_index.t: line 257: vg: käsku ei ole +t/06_vg_index.t: line 257: vg: käsku ei ole +t/06_vg_index.t: line 263: vg: käsku ei ole +t/06_vg_index.t: line 264: vg: käsku ei ole +t/06_vg_index.t: line 265: vg: käsku ei ole +t/06_vg_index.t: line 268: vg: käsku ei ole cat: graph.gbz: No such file or directory t/06_vg_index.t ....... 1..54 @@ -25424,7 +31677,7 @@ # got: '127' # expected: '0' not ok 22 - no warnings about missing variants produced -# got: '48' +# got: '44' # expected: '0' not ok 23 - building an XG index of multiple graphs # got: '127' @@ -27976,6 +34229,7 @@ t/33_vg_mpmap.t: line 152: vg: command not found rm: cannot remove 'xy.xg': No such file or directory rm: cannot remove 'xy.gcsa': No such file or directory +rm: cannot remove 'xy.dist': No such file or directory t/33_vg_mpmap.t ....... 1..21 not ok 1 - MAPQ is 50% without haplotype info @@ -35586,7 +41840,7 @@ Failed tests: 1, 3-10, 12-13, 15-17 t/54_vg_haplotypes.t (Wstat: 0 Tests: 21 Failed: 21) Failed tests: 1-21 -Files=53, Tests=1138, 15 wallclock secs ( 0.66 usr 0.16 sys + 7.82 cusr 4.13 csys = 12.77 CPU) +Files=53, Tests=1138, 11 wallclock secs ( 0.63 usr 0.23 sys + 9.29 cusr 6.83 csys = 16.98 CPU) Result: FAIL make[1]: [debian/rules:76: override_dh_auto_test-arch] Error 1 (ignored) make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' @@ -35627,9 +41881,9 @@ dpkg-shlibdeps: warning: cannot find library libhandlegraph.so needed by debian/vg/usr/lib/vg/vg-avx (ELF format: 'elf64-x86-64' abi: 'ELF:64:l:amd64:0'; RPATH: '') dpkg-shlibdeps: warning: cannot find library libhandlegraph.so needed by debian/vg/usr/lib/vg/vg-ssse3 (ELF format: 'elf64-x86-64' abi: 'ELF:64:l:amd64:0'; RPATH: '') dpkg-shlibdeps: warning: cannot find library libhandlegraph.so needed by debian/vg/usr/lib/vg/vg-sse3 (ELF format: 'elf64-x86-64' abi: 'ELF:64:l:amd64:0'; RPATH: '') -dpkg-shlibdeps: warning: cannot find library libhandlegraph.so needed by debian/vg/usr/lib/vg/vg-plain (ELF format: 'elf64-x86-64' abi: 'ELF:64:l:amd64:0'; RPATH: '') dpkg-shlibdeps: warning: cannot find library libhandlegraph.so needed by debian/vg/usr/lib/vg/vg-avx2 (ELF format: 'elf64-x86-64' abi: 'ELF:64:l:amd64:0'; RPATH: '') dpkg-shlibdeps: warning: cannot find library libhandlegraph.so needed by debian/vg/usr/lib/vg/vg-sse4.1 (ELF format: 'elf64-x86-64' abi: 'ELF:64:l:amd64:0'; RPATH: '') +dpkg-shlibdeps: warning: cannot find library libhandlegraph.so needed by debian/vg/usr/lib/vg/vg-plain (ELF format: 'elf64-x86-64' abi: 'ELF:64:l:amd64:0'; RPATH: '') dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' @@ -35637,8 +41891,8 @@ make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_md5sums dh_builddeb -dpkg-deb: building package 'vg-dbgsym' in '../vg-dbgsym_1.59.0+ds-0.1_amd64.deb'. dpkg-deb: building package 'vg' in '../vg_1.59.0+ds-0.1_amd64.deb'. +dpkg-deb: building package 'vg-dbgsym' in '../vg-dbgsym_1.59.0+ds-0.1_amd64.deb'. dpkg-deb: building package 'vg-docs' in '../vg-docs_1.59.0+ds-0.1_all.deb'. dpkg-genbuildinfo --build=binary -O../vg_1.59.0+ds-0.1_amd64.buildinfo dpkg-genchanges --build=binary -O../vg_1.59.0+ds-0.1_amd64.changes @@ -35647,12 +41901,14 @@ 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/2598675/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2598675/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/2027625 and its subdirectories -I: Current time: Sat Dec 27 10:31:42 -12 2025 -I: pbuilder-time-stamp: 1766874702 +I: removing directory /srv/workspace/pbuilder/2598675 and its subdirectories +I: Current time: Mon Nov 25 07:44:37 +14 2024 +I: pbuilder-time-stamp: 1732470277