Diff of the two buildlogs: -- --- b1/build.log 2025-08-15 21:40:06.645756820 +0000 +++ b2/build.log 2025-08-15 21:42:29.589949553 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Sep 17 16:01:01 -12 2026 -I: pbuilder-time-stamp: 1789704061 +I: Current time: Sat Aug 16 11:40:09 +14 2025 +I: pbuilder-time-stamp: 1755294009 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -32,53 +32,85 @@ dpkg-source: info: applying cmakelists-fixups.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4191687/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3932586/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Aug 15 21:40 /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/3932586/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3932586/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='e98fe6f6459c461b96bbb32de6115884' - 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='4191687' - PS1='# ' - PS2='> ' + INVOCATION_ID=20804588202249e48e7b856b5da0b01b + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3932586 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.AH6srMNN/pbuilderrc_UEAZ --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.AH6srMNN/b1 --logfile b1/build.log libvcflib_1.0.12+dfsg-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.AH6srMNN/pbuilderrc_9UpK --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.AH6srMNN/b2 --logfile b2/build.log libvcflib_1.0.12+dfsg-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4191687/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3932586/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -289,7 +321,7 @@ Get: 141 http://deb.debian.org/debian unstable/main arm64 python3.13-dev arm64 3.13.6-1 [505 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.13.5-1 [26.1 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 python3-pybind11 all 2.13.6-2 [215 kB] -Fetched 60.5 MB in 1s (111 MB/s) +Fetched 60.5 MB in 0s (203 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (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 ... 20002 files and directories currently installed.) @@ -765,8 +797,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Sep 18 04:01:23 UTC 2026. -Universal Time is now: Fri Sep 18 04:01:23 UTC 2026. +Local time is now: Fri Aug 15 21:40:33 UTC 2025. +Universal Time is now: Fri Aug 15 21:40:33 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -888,7 +920,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libvcflib-1.0.12+dfsg/ && 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 > ../libvcflib_1.0.12+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/3932586/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3932586/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libvcflib-1.0.12+dfsg/ && 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 > ../libvcflib_1.0.12+dfsg-1_source.changes dpkg-buildpackage: info: source package libvcflib dpkg-buildpackage: info: source version 1.0.12+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -980,8 +1016,8 @@ -- Using included tabixpp -- WFA using include /usr/include/wfa2lib Pandoc needs to be installed to generate the man pages --- Configuring done (5.3s) --- Generating done (0.3s) +-- Configuring done (7.0s) +-- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: @@ -1008,30 +1044,30 @@ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcflib.dir/build.make CMakeFiles/vcflib.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 0%] Building CXX object CMakeFiles/vcflib.dir/src/legacy.cpp.o -[ 0%] Building CXX object CMakeFiles/vcflib.dir/src/vcf-c-api.cpp.o -[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/vcf-wfa.cpp.o -[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/split.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -Dvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIC -MD -MT CMakeFiles/vcflib.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcflib.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcflib.dir/src/vcf-wfa.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf-wfa.cpp -[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.cpp.o -[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/var.cpp.o -[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/canonicalize.cpp.o +[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.cpp.o +[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/canonicalize.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -Dvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIC -MD -MT CMakeFiles/vcflib.dir/src/canonicalize.cpp.o -MF CMakeFiles/vcflib.dir/src/canonicalize.cpp.o.d -o CMakeFiles/vcflib.dir/src/canonicalize.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/canonicalize.cpp +[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/vcf-c-api.cpp.o +[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/legacy.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -Dvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include 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-I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIC -MD -MT CMakeFiles/vcflib.dir/src/legacy.cpp.o -MF CMakeFiles/vcflib.dir/src/legacy.cpp.o.d -o CMakeFiles/vcflib.dir/src/legacy.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/legacy.cpp -[ 4%] Building CXX object CMakeFiles/vcflib.dir/src/pdflib.cpp.o 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-ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIC -MD -MT CMakeFiles/vcflib.dir/src/pdflib.cpp.o -MF CMakeFiles/vcflib.dir/src/pdflib.cpp.o.d -o CMakeFiles/vcflib.dir/src/pdflib.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/pdflib.cpp [ 6%] Building CXX object CMakeFiles/vcflib.dir/src/LeftAlign.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -Dvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIC -MD -MT CMakeFiles/vcflib.dir/src/LeftAlign.cpp.o -MF CMakeFiles/vcflib.dir/src/LeftAlign.cpp.o.d -o CMakeFiles/vcflib.dir/src/LeftAlign.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/LeftAlign.cpp [ 7%] Building CXX object CMakeFiles/vcflib.dir/src/cigar.cpp.o @@ -1100,150 +1136,158 @@ make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/depend make -f CMakeFiles/bFst.dir/build.make CMakeFiles/bFst.dir/depend make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/depend -make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfecho.dir/DependInfo.cmake "--color=" -make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/depend +make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/DependInfo.cmake "--color=" -make -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/bFst.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/depend cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/pVst.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/hapLrt.dir/DependInfo.cmake "--color=" +make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/depend +make -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/depend +make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/popStats.dir/DependInfo.cmake "--color=" make[4]: Entering directory 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -MF CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o.d -o CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/plotHaps.cpp -[ 24%] Linking CXX executable bFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/bFst.dir/link.txt --verbose=1 -[ 24%] Linking CXX executable pVst -/usr/bin/cmake -E cmake_link_script CMakeFiles/pVst.dir/link.txt --verbose=1 -[ 24%] Linking CXX executable iHS -/usr/bin/cmake -E cmake_link_script CMakeFiles/iHS.dir/link.txt --verbose=1 -[ 24%] Linking CXX executable hapLrt -/usr/bin/cmake -E cmake_link_script CMakeFiles/hapLrt.dir/link.txt --verbose=1 -[ 24%] Linking CXX executable smoother -/usr/bin/cmake -E cmake_link_script CMakeFiles/smoother.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/popStats.dir/link.d CMakeFiles/popStats.dir/src/popStats.cpp.o -o popStats -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/wcFst.dir/link.d CMakeFiles/wcFst.dir/src/wcFst.cpp.o -o wcFst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 24%] Built target popStats +[ 24%] Built target wcFst make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/abba-baba.dir/DependInfo.cmake "--color=" @@ -1273,11 +1307,9 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 24%] Building CXX object CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -MF CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o.d -o CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/abba-baba.cpp -[ 24%] Linking CXX executable pFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/pFst.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/wcFst.dir/link.d CMakeFiles/wcFst.dir/src/wcFst.cpp.o -o wcFst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/popStats.dir/link.d CMakeFiles/popStats.dir/src/popStats.cpp.o -o popStats -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 24%] Built target wcFst +[ 24%] Built target popStats make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/permuteGPAT++.dir/DependInfo.cmake "--color=" @@ -1286,104 +1318,108 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 25%] Building CXX object CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -MF CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o.d -o CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/permuteGPAT++.cpp -[ 26%] Linking CXX executable vcfld -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfld.dir/link.txt --verbose=1 -[ 26%] Linking CXX executable plotHaps -/usr/bin/cmake -E cmake_link_script CMakeFiles/plotHaps.dir/link.txt --verbose=1 +[ 25%] Linking CXX executable smoother +/usr/bin/cmake -E cmake_link_script CMakeFiles/smoother.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/genotypeSummary.dir/link.d CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o -o genotypeSummary -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 26%] Built target genotypeSummary +[ 25%] Built target genotypeSummary make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/permuteSmooth.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 27%] Building CXX object CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o +[ 26%] Building CXX object CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -MF CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o.d -o CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/permuteSmooth.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/bFst.dir/link.d CMakeFiles/bFst.dir/src/bFst.cpp.o -o bFst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 26%] Linking CXX executable pFst +/usr/bin/cmake -E cmake_link_script CMakeFiles/pFst.dir/link.txt --verbose=1 +[ 26%] Linking CXX executable plotHaps +/usr/bin/cmake -E cmake_link_script CMakeFiles/plotHaps.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pVst.dir/link.d CMakeFiles/pVst.dir/src/pVst.cpp.o -o pVst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 27%] Built target bFst +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/sequenceDiversity.dir/link.d CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -o sequenceDiversity -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 26%] Built target sequenceDiversity make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/depend +[ 26%] Built target pVst +make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/normalize-iHS.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/meltEHH.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 28%] Building CXX object CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp 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/build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/meltEHH.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 29%] Building CXX object CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -MF CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o.d -o CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/meltEHH.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pVst.dir/link.d CMakeFiles/pVst.dir/src/pVst.cpp.o -o pVst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 29%] Built target pVst +[ 27%] Building CXX object CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp 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'/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfnullgenofields.dir/DependInfo.cmake "--color=" -[ 29%] Linking CXX executable abba-baba -/usr/bin/cmake -E cmake_link_script CMakeFiles/abba-baba.dir/link.txt --verbose=1 +[ 28%] Building CXX object CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree 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/usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 29%] Built target iHS +[ 28%] Building CXX object CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o -MF CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o.d -o CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfnullgenofields.cpp +[ 28%] Built target iHS make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfaltcount.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/sequenceDiversity.dir/link.d CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -o sequenceDiversity 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-ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -MF CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o.d -o CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfaltcount.cpp +[ 30%] Linking CXX executable vcfld +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfld.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smoother.dir/link.d CMakeFiles/smoother.dir/src/smoother.cpp.o -o smoother -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 29%] Built target sequenceDiversity +[ 30%] Linking CXX executable permuteSmooth +/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteSmooth.dir/link.txt --verbose=1 +[ 30%] Built target smoother make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake 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-ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -MF CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o.d -o CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfaltcount.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 30%] Building CXX object CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -MF CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o.d -o CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfhetcount.cpp -[ 30%] Linking CXX executable permuteSmooth -/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteSmooth.dir/link.txt --verbose=1 +[ 30%] Linking CXX executable abba-baba +/usr/bin/cmake -E cmake_link_script CMakeFiles/abba-baba.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/permuteGPAT++.dir/link.d CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -o permuteGPAT++ -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so 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'/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 30%] Building CXX object CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -MF CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o.d -o CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfhethomratio.cpp [ 30%] Linking CXX executable normalize-iHS /usr/bin/cmake -E cmake_link_script CMakeFiles/normalize-iHS.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pFst.dir/link.d CMakeFiles/pFst.dir/src/pFst.cpp.o -o pFst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 30%] Built target pFst make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/depend -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcffilter.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/build -[ 30%] Building CXX object CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -MF CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o.d -o CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfhethomratio.cpp [ 31%] Building CXX object CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -MF CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o.d -o CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcffilter.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hapLrt.dir/link.d CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -o hapLrt -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 @@ -1397,118 +1433,118 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 32%] Building CXX object CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -MF CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o.d -o CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf2tsv.cpp +[ 32%] Linking CXX executable vcfaltcount +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaltcount.dir/link.txt --verbose=1 +[ 33%] Linking CXX executable vcfhetcount +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhetcount.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plotHaps.dir/link.d CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -o plotHaps -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 32%] Built target plotHaps +[ 33%] Built target plotHaps make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgenotypes.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 32%] Building CXX object CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/normalize-iHS.dir/link.d "CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o" -o normalize-iHS -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -g -O2 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CMakeFiles/vcfnullgenofields.dir/link.txt --verbose=1 +[ 34%] Building CXX object CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o 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'/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 33%] Building CXX object CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o +[ 35%] Building CXX object CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 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/usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 33%] Built target permuteSmooth +[ 35%] Built target normalize-iHS make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcommonsamples.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 34%] Building CXX object CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o +[ 36%] Building CXX object CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -MF CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o.d -o CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfcommonsamples.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include 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'/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfremovesamples.dir/DependInfo.cmake "--color=" -[ 36%] Linking CXX executable vcfhetcount -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhetcount.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 36%] Building CXX object CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -MF CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o.d -o CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfremovesamples.cpp -[ 36%] Linking CXX executable meltEHH -/usr/bin/cmake -E cmake_link_script CMakeFiles/meltEHH.dir/link.txt --verbose=1 [ 37%] Linking CXX executable vcfhethomratio /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhethomratio.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfld.dir/link.d CMakeFiles/vcfld.dir/src/vcfld.cpp.o -o vcfld -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfaltcount.dir/link.d CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -o vcfaltcount -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 37%] Built target vcfld +[ 37%] Built target vcfaltcount make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfkeepsamples.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 37%] Linking CXX executable vcf2tsv -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2tsv.dir/link.txt --verbose=1 [ 37%] Building CXX object CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o +[ 37%] Linking CXX executable meltEHH /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -MF CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o.d -o CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfkeepsamples.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfaltcount.dir/link.d CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -o vcfaltcount -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/cmake -E cmake_link_script CMakeFiles/meltEHH.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfhetcount.dir/link.d CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -o vcfhetcount -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 37%] Built target vcfaltcount +[ 37%] Built target vcfhetcount make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfhetcount.dir/link.d CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -o vcfhetcount -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 37%] Linking CXX executable vcffilter +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffilter.dir/link.txt --verbose=1 +[ 37%] Linking CXX executable vcf2tsv +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2tsv.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfnullgenofields.dir/link.d CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o -o vcfnullgenofields -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 38%] Built target vcfhetcount +[ 37%] Linking CXX executable vcfcommonsamples +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcommonsamples.dir/link.txt --verbose=1 +[ 37%] Built target vcfnullgenofields make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 39%] Building CXX object CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o +[ 38%] Building CXX object CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp 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CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o -o vcfnullgenofields -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfld.dir/link.d CMakeFiles/vcfld.dir/src/vcfld.cpp.o -o vcfld -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 40%] Built target vcfnullgenofields +[ 39%] Linking CXX executable vcfgenotypes +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypes.dir/link.txt --verbose=1 +[ 39%] Built target vcfld make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcffixup.dir/DependInfo.cmake "--color=" -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfhethomratio.dir/link.d CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -o vcfhethomratio -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 40%] Built target vcfhethomratio -[ 41%] Building CXX object CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/depend +[ 40%] Building CXX object CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -MF CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o.d -o CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcffixup.cpp +[ 41%] Linking CXX executable vcfremovesamples +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremovesamples.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfhethomratio.dir/link.d CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -o vcfhethomratio -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 41%] Built target vcfhethomratio +make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfclassify.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' @@ -1516,12 +1552,12 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 42%] Building CXX object CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -MF CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o.d -o CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfclassify.cpp -[ 43%] Linking CXX executable vcfsamplenames -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplenames.dir/link.txt --verbose=1 -[ 43%] Linking CXX executable vcfannotategenotypes +[ 42%] Linking CXX executable vcfannotategenotypes /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotategenotypes.dir/link.txt --verbose=1 -[ 44%] Linking CXX executable vcfkeepsamples +[ 43%] Linking CXX executable vcfkeepsamples /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepsamples.dir/link.txt --verbose=1 +[ 44%] Linking CXX executable vcfsamplenames +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplenames.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfgenotypes.dir/link.d CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -o vcfgenotypes -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 44%] Built target vcfgenotypes @@ -1533,42 +1569,44 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 44%] Building CXX object CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -MF CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o.d -o CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfsamplediff.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcf2tsv.dir/link.d CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -o vcf2tsv -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfremovesamples.dir/link.d CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -o vcfremovesamples -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfcommonsamples.dir/link.d CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -o vcfcommonsamples -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 44%] Built target vcf2tsv +[ 44%] Built target vcfcommonsamples make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake "--color=" -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfsamplenames.dir/link.d CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -o vcfsamplenames -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 44%] Built target vcfremovesamples make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 44%] Building CXX object CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -MF CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o.d -o CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfremoveaberrantgenotypes.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfremovesamples.dir/link.d CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -o vcfremovesamples -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 44%] Built target vcfremovesamples make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfrandom.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/build +make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 44%] Built target vcfsamplenames +[ 44%] Building CXX object CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -MF CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o.d -o CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfrandom.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcf2tsv.dir/link.d CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -o vcf2tsv -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 44%] Built target vcf2tsv make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/depend -[ 44%] Building CXX object CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfflatten.dir/DependInfo.cmake "--color=" -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -MF CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o.d -o CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfremoveaberrantgenotypes.cpp -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 44%] Building CXX object CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -MF CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o.d -o CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfrandom.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfsamplenames.dir/link.d CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -o vcfsamplenames -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 44%] Linking CXX executable vcffixup [ 45%] Building CXX object CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -MF CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o.d -o CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfflatten.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfcommonsamples.dir/link.d CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -o vcfcommonsamples -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 45%] Built target vcfcommonsamples +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffixup.dir/link.txt --verbose=1 +[ 45%] Built target vcfsamplenames make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfprimers.dir/DependInfo.cmake "--color=" @@ -1577,6 +1615,8 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 45%] Building CXX object CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -MF CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o.d -o CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfprimers.cpp +[ 45%] Linking CXX executable vcfgenotypecompare +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypecompare.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfkeepsamples.dir/link.d CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -o vcfkeepsamples -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 45%] Built target vcfkeepsamples @@ -1586,12 +1626,10 @@ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 45%] Building CXX object CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -MF CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o.d -o CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfnumalt.cpp -[ 45%] Linking CXX executable vcfgenotypecompare -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypecompare.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/meltEHH.dir/link.d CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -o meltEHH -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 45%] Building CXX object CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -MF CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o.d -o CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfnumalt.cpp [ 45%] Built target meltEHH make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' @@ -1601,6 +1639,8 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 45%] Building CXX object CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -MF CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o.d -o CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfintersect.cpp +[ 45%] Linking CXX executable vcfclassify +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfclassify.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcffilter.dir/link.d CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -o vcffilter -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 45%] Built target vcffilter @@ -1612,101 +1652,97 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 46%] Building CXX object CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -MF CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o.d -o CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfannotate.cpp -[ 46%] Linking CXX executable vcfclassify -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfclassify.dir/link.txt --verbose=1 -[ 46%] Linking CXX executable vcffixup -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffixup.dir/link.txt --verbose=1 -[ 47%] Linking CXX executable vcfsamplediff -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplediff.dir/link.txt --verbose=1 -[ 48%] Linking CXX executable vcfrandom -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandom.dir/link.txt --verbose=1 -[ 49%] Linking CXX executable vcfprimers -[ 50%] Linking CXX executable vcfremoveaberrantgenotypes -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfprimers.dir/link.txt --verbose=1 +[ 47%] Linking CXX executable vcfremoveaberrantgenotypes /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremoveaberrantgenotypes.dir/link.txt --verbose=1 -[ 51%] Linking CXX executable vcfnumalt -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfnumalt.dir/link.txt --verbose=1 +[ 48%] Linking CXX executable vcfprimers +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfprimers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfclassify.dir/link.d CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -o vcfclassify -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 51%] Built target vcfclassify +[ 48%] Built target vcfclassify make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/depend -[ 51%] Linking CXX executable vcfflatten make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfflatten.dir/link.txt --verbose=1 cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu 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vcfnumalt +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfnumalt.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcffixup.dir/link.d CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -o vcffixup -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' 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/usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 52%] Built target vcfannotategenotypes +[ 51%] Built target vcfremoveaberrantgenotypes +[ 51%] Built target vcfprimers make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/depend +make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu 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-I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -MF CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o.d -o CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfaddinfo.cpp [ 52%] Building CXX object CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -MF CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o.d -o 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'/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfnumalt.dir/link.d CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -o vcfnumalt -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfsamplediff.dir/link.d CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -o vcfsamplediff -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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'/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfafpath.dir/DependInfo.cmake "--color=" -[ 52%] Built target vcfsamplediff -make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/depend -[ 52%] Built target vcfnumalt -make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix 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'/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 53%] Building CXX object CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -MF CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o.d -o CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfafpath.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfsamplediff.dir/link.d CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -o vcfsamplediff -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 53%] Built target vcfsamplediff +make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcountalleles.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 54%] Building CXX object CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -MF CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o.d -o CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfcountalleles.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfnumalt.dir/link.d CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -o vcfnumalt -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 54%] Built target vcfnumalt +make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcflength.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 53%] Building CXX object CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -[ 54%] Building CXX object CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -MF CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o.d -o CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfcountalleles.cpp -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -MF CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o.d -o CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfafpath.cpp [ 54%] Building CXX object CMakeFiles/vcflength.dir/src/vcflength.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcflength.dir/src/vcflength.cpp.o -MF CMakeFiles/vcflength.dir/src/vcflength.cpp.o.d -o CMakeFiles/vcflength.dir/src/vcflength.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcflength.cpp +[ 54%] Linking CXX executable vcfannotate +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotate.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfrandom.dir/link.d CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -o vcfrandom -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 54%] Built target vcfrandom @@ -1718,95 +1754,96 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 55%] Building CXX object CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -MF CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o.d -o CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfdistance.cpp -[ 56%] Linking CXX executable vcfoverlay +[ 56%] Linking CXX executable vcfkeepinfo +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepinfo.dir/link.txt --verbose=1 +[ 57%] Linking CXX executable vcfoverlay /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfoverlay.dir/link.txt --verbose=1 +[ 57%] Linking CXX executable vcfaddinfo +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaddinfo.dir/link.txt --verbose=1 +[ 58%] Linking CXX executable vcfintersect +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfintersect.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -MF CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o.d -o 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/usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 61%] Built target vcfcountalleles [ 61%] Built target vcfkeepinfo make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfglxgt.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -make -f 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-std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -MF CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o.d -o CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfglxgt.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfoverlay.dir/link.d CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -o vcfoverlay -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 61%] Built target vcfoverlay make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcheck.dir/DependInfo.cmake "--color=" -[ 61%] Linking CXX executable vcfdistance -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfdistance.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 61%] Building CXX object CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar 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CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -o vcfafpath -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 62%] Built target vcflength +[ 62%] Built target vcfafpath make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg 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-ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfkeepgeno.dir/link.d CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -o vcfkeepgeno -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/build -make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 62%] Built target vcfkeepgeno +make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfuniq.dir/DependInfo.cmake "--color=" [ 62%] Building CXX object CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -[ 62%] Building CXX object CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -MF CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o.d -o CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfstreamsort.cpp +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 62%] Building CXX object CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -MF CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o.d -o CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfuniq.cpp -[ 62%] Linking CXX executable vcfentropy -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfentropy.dir/link.txt --verbose=1 +[ 62%] Linking CXX executable vcfdistance +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfdistance.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfoverlay.dir/link.d CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -o vcfoverlay -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 62%] Built target vcfoverlay make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake "--color=" @@ -1815,9 +1852,6 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 62%] Building CXX object CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -MF CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o.d -o CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfuniqalleles.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfafpath.dir/link.d CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -o vcfafpath -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 62%] Built target vcfafpath make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfremap.dir/DependInfo.cmake "--color=" @@ -1826,65 +1860,67 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 62%] Building CXX object CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -MF CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o.d -o CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfremap.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfkeepgeno.dir/link.d CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -o vcfkeepgeno -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 63%] Linking CXX executable vcfrandomsample +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandomsample.dir/link.txt --verbose=1 +[ 63%] Linking CXX executable vcfentropy +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfentropy.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcflength.dir/link.d CMakeFiles/vcflength.dir/src/vcflength.cpp.o -o vcflength -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 62%] Built target vcfkeepgeno +[ 63%] Built target vcflength make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcf2fasta.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 63%] Building CXX object CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o +[ 64%] Building CXX object CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree 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CMakeFiles/vcfcheck.dir/link.txt --verbose=1 [ 64%] Building CXX object CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT 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/usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfrandomsample.dir/link.d CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -o vcfrandomsample -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving 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make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 68%] Building CXX object CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o +[ 70%] Building CXX object CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -MF CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o.d -o CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfevenregions.cpp -[ 69%] Linking CXX executable vcfuniqalleles -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniqalleles.dir/link.txt --verbose=1 -[ 70%] Linking CXX executable vcfstreamsort -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstreamsort.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfrandomsample.dir/link.d CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -o vcfrandomsample -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfcheck.dir/link.d CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -o vcfcheck -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 70%] Built target vcfrandomsample +[ 70%] Built target vcfcheck make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcat.dir/DependInfo.cmake "--color=" @@ -1893,22 +1929,20 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 71%] Building CXX object CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -MF CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o.d -o CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfcat.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfuniq.dir/link.d CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -o vcfuniq -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfentropy.dir/link.d CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -o vcfentropy -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 71%] Built target vcfuniq +[ 71%] Built target vcfentropy make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgenosummarize.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/build -[ 71%] Linking CXX executable vcf2fasta make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2fasta.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfcheck.dir/link.d CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -o vcfcheck -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 72%] Building CXX object CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto 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/usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 72%] Built target vcfintersect make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgenosamplenames.dir/DependInfo.cmake "--color=" @@ -1917,23 +1951,23 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 73%] Building CXX object CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -MF CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o.d -o CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfgenosamplenames.cpp -[ 74%] Linking CXX executable vcfremap -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremap.dir/link.txt --verbose=1 -[ 74%] Linking CXX executable vcfbreakmulti -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfbreakmulti.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfglxgt.dir/link.d CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -o vcfglxgt -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 75%] Linking CXX executable vcfsitesummarize -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsitesummarize.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfuniq.dir/link.d CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -o vcfuniq -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 75%] Built target vcfglxgt +[ 73%] Built target vcfuniq make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgeno2haplo.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 76%] Building CXX object CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o +[ 74%] Building CXX object CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o -MF CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o.d -o CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfgeno2haplo.cpp +[ 74%] Linking CXX executable vcf2fasta +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2fasta.dir/link.txt --verbose=1 +[ 75%] Linking CXX executable vcfsitesummarize +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsitesummarize.dir/link.txt --verbose=1 +[ 76%] Linking CXX executable vcfremap +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremap.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfuniqalleles.dir/link.d CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -o vcfuniqalleles -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 76%] Built target vcfuniqalleles @@ -1945,9 +1979,13 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 76%] Building CXX object CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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/usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 76%] Linking CXX executable vcfbreakmulti +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfbreakmulti.dir/link.txt --verbose=1 +[ 76%] Linking CXX executable vcfcat +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcat.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfglxgt.dir/link.d CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -o vcfglxgt -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 76%] Built target vcfintersect +[ 76%] Built target vcfglxgt make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcombine.dir/DependInfo.cmake "--color=" @@ -1956,84 +1994,84 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 77%] Building CXX object CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -o vcfstreamsort -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfsitesummarize.dir/link.d CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -o vcfsitesummarize -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 77%] Built target vcfsitesummarize +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 77%] Built target vcfstreamsort make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/depend +[ 77%] Linking CXX executable vcfevenregions make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgeno2alleles.dir/DependInfo.cmake "--color=" -[ 77%] Linking CXX executable vcfgenosummarize -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosummarize.dir/link.txt --verbose=1 +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfevenregions.dir/link.txt --verbose=1 +[ 77%] Built target vcfsitesummarize +make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfindex.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 77%] Building CXX object CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -MF CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o.d -o CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfindex.cpp [ 78%] Building CXX object CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -MF CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o.d -o CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfgeno2alleles.cpp +[ 78%] Linking CXX executable vcfgenosummarize +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosummarize.dir/link.txt --verbose=1 [ 78%] Linking CXX executable vcfgenosamplenames /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosamplenames.dir/link.txt --verbose=1 -[ 79%] Linking CXX executable vcfleftalign -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcf2fasta.dir/link.d CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -o vcf2fasta -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfleftalign.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfstreamsort.dir/link.d CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -o vcfstreamsort -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 79%] Built target vcf2fasta -make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfindex.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfcat.dir/link.d CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -o vcfcat -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 79%] Built target vcfstreamsort +[ 78%] Built target vcfcat make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/depend -[ 79%] Building CXX object CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -MF CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o.d -o CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfindex.cpp cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcf2dag.dir/DependInfo.cmake "--color=" -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfevenregions.dir/link.d CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -o vcfevenregions -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 79%] Built target vcfevenregions -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfcat.dir/link.d CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -o vcfcat -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 79%] Building CXX object CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -MF CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o.d -o CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf2dag.cpp +[ 80%] Linking CXX executable vcfleftalign +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfleftalign.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfbreakmulti.dir/link.d CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -o vcfbreakmulti -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 80%] Built target vcfbreakmulti make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/depend -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfbreakmulti.dir/link.d CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -o vcfbreakmulti -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfsample2info.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 80%] Building CXX object CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -MF CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o.d -o CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf2dag.cpp -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 80%] Built target vcfcat -make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 80%] Built target vcfbreakmulti -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfqual2info.dir/DependInfo.cmake "--color=" -make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/depend [ 80%] Building CXX object CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfinfo2qual.dir/DependInfo.cmake "--color=" /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -MF CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o.d -o CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfsample2info.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcf2fasta.dir/link.d CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -o vcf2fasta -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/build +[ 80%] Built target vcf2fasta +make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfqual2info.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/build +make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 80%] Building CXX object CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -MF CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o.d -o CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfqual2info.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfgenosamplenames.dir/link.d CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -o vcfgenosamplenames -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfevenregions.dir/link.d CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -o vcfevenregions -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 80%] Built target vcfevenregions +make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfinfo2qual.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 80%] Building CXX object CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -MF CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o.d -o CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfinfo2qual.cpp +[ 80%] Linking CXX executable vcfgeno2haplo +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2haplo.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfgenosamplenames.dir/link.d CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -o vcfgenosamplenames -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 80%] Built target vcfgenosamplenames make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' @@ -2043,146 +2081,149 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 80%] Building CXX object CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -MF CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o.d -o CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfglbound.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfremap.dir/link.d CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -o vcfremap -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 80%] Linking CXX executable vcfgeno2alleles +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2alleles.dir/link.txt --verbose=1 +[ 81%] Linking CXX executable vcfindex +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfindex.dir/link.txt --verbose=1 +[ 81%] Linking CXX executable vcfcombine +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcombine.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfgenosummarize.dir/link.d CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -o vcfgenosummarize -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 80%] Built target vcfremap +[ 81%] Built target vcfgenosummarize make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/depend -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2haplo.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake "--color=" +[ 81%] Linking CXX executable vcf2dag +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2dag.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 81%] Building CXX object CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o +[ 82%] Building CXX object CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -MF CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o.d -o CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfcreatemulti.cpp -[ 81%] Linking CXX executable vcfcombine -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcombine.dir/link.txt --verbose=1 -[ 82%] Linking CXX executable vcfqual2info -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfqual2info.dir/link.txt --verbose=1 -[ 83%] Linking CXX executable vcfinfo2qual -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfinfo2qual.dir/link.txt --verbose=1 -[ 84%] Linking CXX executable vcfsample2info -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsample2info.dir/link.txt --verbose=1 -[ 85%] Linking CXX executable vcfindex -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfindex.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfgeno2alleles.dir/link.d CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -o vcfgeno2alleles -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 85%] Built target vcfgeno2alleles +[ 82%] Built target vcfgeno2alleles make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfallelicprimitives.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 83%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -MF CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o.d -o CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfallelicprimitives.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfleftalign.dir/link.d CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -o vcfleftalign -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so 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88%] Linking CXX executable vcfinfosummarize -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfinfosummarize.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfinfo2qual.dir/link.d CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -o vcfinfo2qual -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 86%] Linking CXX executable vcfqual2info 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-DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf-wfa.cpp -[ 90%] Linking CXX executable vcfcreatemulti -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcreatemulti.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcf2dag.dir/link.d CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -o vcf2dag -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 90%] Built target vcf2dag make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfroc.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 90%] Building CXX object CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o +[ 89%] Building CXX object CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto 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/usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 89%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/legacy.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcleancomplex.dir/src/legacy.cpp.o -MF CMakeFiles/vcfcleancomplex.dir/src/legacy.cpp.o.d -o CMakeFiles/vcfcleancomplex.dir/src/legacy.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/legacy.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfinfosummarize.dir/link.d CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -o vcfinfosummarize -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 90%] Built target vcfinfosummarize +[ 89%] Built target vcfsample2info make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfstats.dir/DependInfo.cmake "--color=" -/usr/bin/c++ -g -O2 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make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 90%] Built target vcfsample2info +[ 89%] Building CXX object CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfstats.dir/src/legacy.cpp.o -MF CMakeFiles/vcfstats.dir/src/legacy.cpp.o.d -o CMakeFiles/vcfstats.dir/src/legacy.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/legacy.cpp +[ 91%] Building CXX object CMakeFiles/vcfparsealts.dir/src/legacy.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfparsealts.dir/src/legacy.cpp.o -MF CMakeFiles/vcfparsealts.dir/src/legacy.cpp.o.d -o CMakeFiles/vcfparsealts.dir/src/legacy.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/legacy.cpp +[ 91%] Linking CXX executable vcfcreatemulti +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcreatemulti.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfglbound.dir/link.d CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -o vcfglbound -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 91%] Built target vcfglbound +[ 92%] Building CXX object CMakeFiles/vcfroc.dir/src/legacy.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp 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-flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfinfosummarize.dir/link.d CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -o vcfinfosummarize -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 92%] Built target vcfinfosummarize +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfcombine.dir/link.d CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -o vcfcombine -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 93%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf-wfa.cpp +[ 93%] Built target vcfcombine make -f CMakeFiles/vcfwave.dir/build.make CMakeFiles/vcfwave.dir/depend -[ 90%] Building CXX object CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfwave.dir/DependInfo.cmake "--color=" -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -MF CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o.d -o CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfstats.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfwave.dir/build.make CMakeFiles/vcfwave.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 90%] Building CXX object CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o +[ 93%] Building CXX object CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o -MF CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o.d -o CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfwave.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfcombine.dir/link.d CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -o vcfcombine -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 90%] Built target vcfcombine -[ 91%] Building CXX object CMakeFiles/vcfstats.dir/src/legacy.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfstats.dir/src/legacy.cpp.o -MF CMakeFiles/vcfstats.dir/src/legacy.cpp.o.d -o CMakeFiles/vcfstats.dir/src/legacy.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/legacy.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfglbound.dir/link.d CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -o vcfglbound -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[ 92%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf-wfa.cpp -[ 92%] Built target vcfglbound -[ 92%] Building CXX object CMakeFiles/vcfstats.dir/src/vcf-wfa.cpp.o +[ 93%] Building CXX object CMakeFiles/vcfstats.dir/src/vcf-wfa.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfstats.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfstats.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfstats.dir/src/vcf-wfa.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf-wfa.cpp -[ 92%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/legacy.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong 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/usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfwave.dir/src/legacy.cpp.o -MF CMakeFiles/vcfwave.dir/src/legacy.cpp.o.d -o CMakeFiles/vcfwave.dir/src/legacy.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/legacy.cpp -[ 94%] Building CXX object CMakeFiles/vcfroc.dir/src/legacy.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfroc.dir/src/legacy.cpp.o -MF CMakeFiles/vcfroc.dir/src/legacy.cpp.o.d -o CMakeFiles/vcfroc.dir/src/legacy.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/legacy.cpp +[ 94%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf-wfa.cpp +[ 94%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf-wfa.cpp +[ 94%] Building CXX object CMakeFiles/vcfroc.dir/src/vcf-wfa.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfroc.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfroc.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfroc.dir/src/vcf-wfa.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf-wfa.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfcreatemulti.dir/link.d CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -o vcfcreatemulti -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[ 94%] Built target vcfcreatemulti make -f CMakeFiles/pyvcflib.dir/build.make CMakeFiles/pyvcflib.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/CMakeFiles/pyvcflib.dir/DependInfo.cmake "--color=" @@ -2191,50 +2232,45 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [ 95%] Building CXX object CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -Dpyvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/python3.13 -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIC -fvisibility=hidden -MD -MT CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o -MF CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o.d -o CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/pythonffi.cpp +[ 96%] Building CXX object CMakeFiles/vcfwave.dir/src/legacy.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfwave.dir/src/legacy.cpp.o -MF CMakeFiles/vcfwave.dir/src/legacy.cpp.o.d -o CMakeFiles/vcfwave.dir/src/legacy.cpp.o -c 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vcfgeno2haplo -[ 95%] Building CXX object CMakeFiles/vcfwave.dir/src/vcf-wfa.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfcreatemulti.dir/link.d CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -o vcfcreatemulti -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 96%] Built target vcfgeno2haplo +[ 96%] Building CXX object CMakeFiles/vcfwave.dir/src/vcf-wfa.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfwave.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfwave.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfwave.dir/src/vcf-wfa.cpp.o -c 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-fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfroc.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfroc.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfroc.dir/src/vcf-wfa.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf-wfa.cpp -[ 96%] Linking CXX executable vcfparsealts -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfparsealts.dir/link.txt --verbose=1 -[ 97%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" -DVERSION=\"1.0.10\" -I/build/reproducible-path/libvcflib-1.0.12+dfsg/include -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar -I/build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/tabixpp -I/include/wfa2lib -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o -MF CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o.d -o CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf-wfa.cpp -[ 98%] Linking CXX executable vcfstats +[ 96%] Linking CXX executable vcfallelicprimitives +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfallelicprimitives.dir/link.txt --verbose=1 +[ 97%] Linking CXX executable vcfstats /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstats.dir/link.txt --verbose=1 -[ 98%] Linking CXX executable vcfcleancomplex +[ 97%] Linking CXX executable vcfcleancomplex /usr/bin/cmake -E cmake_link_script 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CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o CMakeFiles/vcfparsealts.dir/src/legacy.cpp.o "CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o" -o vcfparsealts -Wl,-rpath,"\$ORIGIN" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libwfa2.so /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[100%] Built target vcfparsealts +[100%] Linking CXX executable vcfwave +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfwave.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfstats.dir/link.d CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o CMakeFiles/vcfstats.dir/src/legacy.cpp.o "CMakeFiles/vcfstats.dir/src/vcf-wfa.cpp.o" -o vcfstats -Wl,-rpath,"\$ORIGIN" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libwfa2.so /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [100%] Built target vcfstats +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfallelicprimitives.dir/link.d CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o CMakeFiles/vcfallelicprimitives.dir/src/legacy.cpp.o "CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o" -o vcfallelicprimitives -Wl,-rpath,"\$ORIGIN" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libwfa2.so /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfcleancomplex.dir/link.d CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o CMakeFiles/vcfcleancomplex.dir/src/legacy.cpp.o "CMakeFiles/vcfcleancomplex.dir/src/vcf-wfa.cpp.o" -o vcfcleancomplex -Wl,-rpath,"\$ORIGIN" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libwfa2.so /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[100%] Built target vcfallelicprimitives [100%] Built target vcfcleancomplex +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfroc.dir/link.d CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o CMakeFiles/vcfroc.dir/src/legacy.cpp.o "CMakeFiles/vcfroc.dir/src/vcf-wfa.cpp.o" -o vcfroc -Wl,-rpath,"\$ORIGIN" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libwfa2.so /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' [100%] Linking CXX shared module pyvcflib.cpython-313-aarch64-linux-gnu.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfparsealts.dir/link.d CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o CMakeFiles/vcfparsealts.dir/src/legacy.cpp.o "CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o" -o vcfparsealts -Wl,-rpath,"\$ORIGIN" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libwfa2.so /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 /usr/bin/cmake -E cmake_link_script CMakeFiles/pyvcflib.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfwave.dir/link.d CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o CMakeFiles/vcfwave.dir/src/legacy.cpp.o "CMakeFiles/vcfwave.dir/src/vcf-wfa.cpp.o" -o vcfwave -Wl,-rpath,"\$ORIGIN" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libwfa2.so /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[100%] Built target vcfwave -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfroc.dir/link.d CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o CMakeFiles/vcfroc.dir/src/legacy.cpp.o "CMakeFiles/vcfroc.dir/src/vcf-wfa.cpp.o" -o vcfroc -Wl,-rpath,"\$ORIGIN" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libwfa2.so /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' +[100%] Built target vcfparsealts [100%] Built target vcfroc -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfallelicprimitives.dir/link.d CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o CMakeFiles/vcfallelicprimitives.dir/src/legacy.cpp.o "CMakeFiles/vcfallelicprimitives.dir/src/vcf-wfa.cpp.o" -o vcfallelicprimitives -Wl,-rpath,"\$ORIGIN" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libwfa2.so /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfwave.dir/link.d CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o CMakeFiles/vcfwave.dir/src/legacy.cpp.o "CMakeFiles/vcfwave.dir/src/vcf-wfa.cpp.o" -o vcfwave -Wl,-rpath,"\$ORIGIN" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libwfa2.so /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' -[100%] Built target vcfallelicprimitives +[100%] Built target vcfwave /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,--dependency-file=CMakeFiles/pyvcflib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o pyvcflib.cpython-313-aarch64-linux-gnu.so CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o -Wl,-rpath,"\$ORIGIN:" libvcflib.so.2 -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libwfa2.so /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 /usr/bin/strip /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu/pyvcflib.cpython-313-aarch64-linux-gnu.so make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-aarch64-linux-gnu' @@ -2251,27 +2287,27 @@ cd test && ctest . Test project /build/reproducible-path/libvcflib-1.0.12+dfsg/test Start 1: realign -1/9 Test #1: realign .......................... Passed 0.09 sec +1/9 Test #1: realign .......................... Passed 0.11 sec Start 2: pyvcflib -2/9 Test #2: pyvcflib ......................... Passed 0.12 sec +2/9 Test #2: pyvcflib ......................... Passed 0.11 sec Start 3: vcflib-api -3/9 Test #3: vcflib-api ....................... Passed 0.12 sec +3/9 Test #3: vcflib-api ....................... Passed 0.08 sec Start 4: vcf2tsv -4/9 Test #4: vcf2tsv .......................... Passed 0.18 sec +4/9 Test #4: vcf2tsv .......................... Passed 0.15 sec Start 5: vcfallelicprimitives -5/9 Test #5: vcfallelicprimitives ............. Passed 1.01 sec +5/9 Test #5: vcfallelicprimitives ............. Passed 0.89 sec Start 6: vcfwave -6/9 Test #6: vcfwave .......................... Passed 0.44 sec +6/9 Test #6: vcfwave .......................... Passed 0.41 sec Start 7: vcffilter -7/9 Test #7: vcffilter ........................ Passed 0.18 sec +7/9 Test #7: vcffilter ........................ Passed 0.21 sec Start 8: vcfnulldotslashdot -8/9 Test #8: vcfnulldotslashdot ............... Passed 0.13 sec +8/9 Test #8: vcfnulldotslashdot ............... Passed 0.12 sec Start 9: doc/vcfintersect -9/9 Test #9: doc/vcfintersect ................. Passed 0.10 sec +9/9 Test #9: doc/vcfintersect ................. Passed 0.07 sec 100% tests passed, 0 tests failed out of 9 -Total Test time (real) = 2.37 sec +Total Test time (real) = 2.17 sec cd .. && rm -f build make[1]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg' create-stamp debian/debhelper-build-stamp @@ -2661,10 +2697,10 @@ dpkg-gencontrol: warning: package libvcflib-tools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake -dpkg-deb: building package 'libvcflib-tools' in '../libvcflib-tools_1.0.12+dfsg-1_arm64.deb'. -dpkg-deb: building package 'libvcflib2' in '../libvcflib2_1.0.12+dfsg-1_arm64.deb'. dpkg-deb: building package 'libvcflib2-dbgsym' in '../libvcflib2-dbgsym_1.0.12+dfsg-1_arm64.deb'. dpkg-deb: building package 'libvcflib-dev' in '../libvcflib-dev_1.0.12+dfsg-1_arm64.deb'. +dpkg-deb: building package 'libvcflib2' in '../libvcflib2_1.0.12+dfsg-1_arm64.deb'. +dpkg-deb: building package 'libvcflib-tools' in '../libvcflib-tools_1.0.12+dfsg-1_arm64.deb'. dpkg-deb: building package 'libvcflib-tools-dbgsym' in '../libvcflib-tools-dbgsym_1.0.12+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libvcflib_1.0.12+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../libvcflib_1.0.12+dfsg-1_arm64.changes @@ -2673,12 +2709,14 @@ 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/3932586/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3932586/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/4191687 and its subdirectories -I: Current time: Thu Sep 17 16:03:05 -12 2026 -I: pbuilder-time-stamp: 1789704185 +I: removing directory /srv/workspace/pbuilder/3932586 and its subdirectories +I: Current time: Sat Aug 16 11:42:28 +14 2025 +I: pbuilder-time-stamp: 1755294148