Diff of the two buildlogs: -- --- b1/build.log 2025-02-17 00:18:20.643368539 +0000 +++ b2/build.log 2025-02-17 00:22:05.393234646 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Feb 16 12:14:11 -12 2025 -I: pbuilder-time-stamp: 1739751251 +I: Current time: Sun Mar 22 20:41:23 +14 2026 +I: pbuilder-time-stamp: 1774161683 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ 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/2924260/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/337771/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 22 06:41 /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/337771/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/337771/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='e2f7916541094f9dbc4a65f72bb797c4' - 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='2924260' - PS1='# ' - PS2='> ' + INVOCATION_ID=ffdcd61e11a442e9acec0869a1518bff + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=337771 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.bYQnS4YU/pbuilderrc_JV83 --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.bYQnS4YU/b1 --logfile b1/build.log libvcflib_1.0.12+dfsg-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.bYQnS4YU/pbuilderrc_jzWl --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.bYQnS4YU/b2 --logfile b2/build.log libvcflib_1.0.12+dfsg-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2924260/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/337771/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: 142 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.2-1 [507 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.1-2 [26.1 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 python3-pybind11 all 2.13.6-2 [215 kB] -Fetched 72.7 MB in 22s (3300 kB/s) +Fetched 72.7 MB in 1s (58.8 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:amd64. (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 ... 19806 files and directories currently installed.) @@ -768,8 +800,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Feb 17 00:15:46 UTC 2025. -Universal Time is now: Mon Feb 17 00:15:46 UTC 2025. +Local time is now: Sun Mar 22 06:42:27 UTC 2026. +Universal Time is now: Sun Mar 22 06:42:27 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -892,7 +924,11 @@ 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/337771/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/337771/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 @@ -984,8 +1020,8 @@ -- Using included tabixpp -- WFA using include /usr/include/wfa2lib Pandoc needs to be installed to generate the man pages --- Configuring done (6.5s) --- Generating done (0.5s) +-- Configuring done (13.7s) +-- Generating done (1.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -1000,7 +1036,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg' dh_auto_build - cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/libvcflib-1.0.12+dfsg -B/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -1012,40 +1048,38 @@ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu' -[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/Variant.cpp.o -[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/legacy.cpp.o -[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/vcf-wfa.cpp.o -[ 4%] Building CXX object CMakeFiles/vcflib.dir/src/pdflib.cpp.o -[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/vcf-c-api.cpp.o -[ 4%] Building CXX object CMakeFiles/vcflib.dir/src/cdflib.cpp.o -[ 4%] Building CXX object CMakeFiles/vcflib.dir/src/canonicalize.cpp.o -[ 4%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.cpp.o -[ 5%] Building CXX object CMakeFiles/vcflib.dir/src/split.cpp.o -[ 5%] Building CXX object CMakeFiles/vcflib.dir/src/var.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 -fcf-protection -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 +[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/vcf-wfa.cpp.o +[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.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 -fcf-protection -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 -/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 -fcf-protection -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-c-api.cpp.o -MF CMakeFiles/vcflib.dir/src/vcf-c-api.cpp.o.d -o CMakeFiles/vcflib.dir/src/vcf-c-api.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf-c-api.cpp -/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 -fcf-protection -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/Variant.cpp.o -MF CMakeFiles/vcflib.dir/src/Variant.cpp.o.d -o CMakeFiles/vcflib.dir/src/Variant.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/Variant.cpp +[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/legacy.cpp.o +[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/canonicalize.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" 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-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -fPIC -MD -MT CMakeFiles/vcflib.dir/contrib/c-progress-bar/progress.c.o -MF CMakeFiles/vcflib.dir/contrib/c-progress-bar/progress.c.o.d -o CMakeFiles/vcflib.dir/contrib/c-progress-bar/progress.c.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar/progress.c -[ 8%] Building C object CMakeFiles/vcflib.dir/contrib/filevercmp/filevercmp.c.o -/usr/bin/cc -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -fPIC -MD -MT CMakeFiles/vcflib.dir/contrib/filevercmp/filevercmp.c.o -MF 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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 -fcf-protection -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/split.cpp.o -MF CMakeFiles/vcflib.dir/src/split.cpp.o.d -o CMakeFiles/vcflib.dir/src/split.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/split.cpp /build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar/progress.c: In function 'print_timedelta': /build/reproducible-path/libvcflib-1.0.12+dfsg/contrib/c-progress-bar/progress.c:79:28: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 79 | fprintf(stderr,"%lluh %llum %llus ", hours, minutes, seconds); @@ -1094,6 +1128,8 @@ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu +[ 8%] Building CXX 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'/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/pVst.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-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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'/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/popStats.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/wcFst.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/iHS.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/wcFst.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/popStats.dir/DependInfo.cmake "--color=" make -f CMakeFiles/segmentFst.dir/build.make CMakeFiles/segmentFst.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/segmentFst.dir/DependInfo.cmake "--color=" make -f CMakeFiles/segmentIhs.dir/build.make CMakeFiles/segmentIhs.dir/depend +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/segmentFst.dir/DependInfo.cmake "--color=" +make -f CMakeFiles/genotypeSummary.dir/build.make CMakeFiles/genotypeSummary.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/segmentIhs.dir/DependInfo.cmake "--color=" -make -f CMakeFiles/genotypeSummary.dir/build.make CMakeFiles/genotypeSummary.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/genotypeSummary.dir/DependInfo.cmake "--color=" make -f CMakeFiles/sequenceDiversity.dir/build.make CMakeFiles/sequenceDiversity.dir/depend +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/genotypeSummary.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +make -f 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'/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/pFst.dir/DependInfo.cmake "--color=" make -f CMakeFiles/smoother.dir/build.make CMakeFiles/smoother.dir/depend -make -f CMakeFiles/vcfld.dir/build.make CMakeFiles/vcfld.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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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'/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfld.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/depend +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/smoother.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu 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/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/plotHaps.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfld.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/depend +make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/build make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make[4]: 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'/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 10%] Building CXX object CMakeFiles/bFst.dir/src/bFst.cpp.o make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 11%] Building CXX object CMakeFiles/pVst.dir/src/pVst.cpp.o +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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 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CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/build -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 16%] Building CXX object CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/popStats.dir/src/popStats.cpp.o -MF CMakeFiles/popStats.dir/src/popStats.cpp.o.d -o CMakeFiles/popStats.dir/src/popStats.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/popStats.cpp +make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/depend /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 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/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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o -MF CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o.d -o CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/segmentIhs.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 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/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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/pFst.dir/src/pFst.cpp.o -MF CMakeFiles/pFst.dir/src/pFst.cpp.o.d -o CMakeFiles/pFst.dir/src/pFst.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/pFst.cpp -[ 21%] Building CXX object CMakeFiles/vcfld.dir/src/vcfld.cpp.o -make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/build +make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 22%] Building CXX object CMakeFiles/smoother.dir/src/smoother.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfld.dir/src/vcfld.cpp.o -MF CMakeFiles/vcfld.dir/src/vcfld.cpp.o.d -o CMakeFiles/vcfld.dir/src/vcfld.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfld.cpp -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.10\" 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/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcommonsamples.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -MF CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o.d -o CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/sequenceDiversity.cpp +make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/depend +[ 20%] Building CXX object CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o +make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/depend +make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/build -[ 22%] 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 -fcf-protection -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 +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfremovesamples.dir/DependInfo.cmake "--color=" +make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/depend +make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 24%] Building CXX object CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -[ 24%] Building CXX 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CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/permuteGPAT++.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 -fcf-protection -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 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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 -fcf-protection -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 -[ 27%] Linking CXX executable permuteSmooth -/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteSmooth.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 -fcf-protection -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/segmentFst.dir/link.d CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o -o segmentFst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 27%] Built target segmentFst -make -f CMakeFiles/vcfnullgenofields.dir/build.make CMakeFiles/vcfnullgenofields.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfnullgenofields.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfkeepsamples.dir/DependInfo.cmake "--color=" +[ 21%] Building CXX object CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o +make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/build +/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 -fcf-protection -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 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfnullgenofields.dir/build.make CMakeFiles/vcfnullgenofields.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 27%] 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 -fcf-protection -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 -/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 -fcf-protection -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/dumpContigsFromHeader.dir/link.d CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -o dumpContigsFromHeader -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 27%] Built target dumpContigsFromHeader -make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu 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-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 -fcf-protection -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 -[ 29%] Linking CXX executable wcFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/wcFst.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 -fcf-protection -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/segmentIhs.dir/link.d CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o -o segmentIhs -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfsamplenames.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 -fcf-protection -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 +[ 23%] Building CXX object CMakeFiles/pFst.dir/src/pFst.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/pFst.dir/src/pFst.cpp.o -MF CMakeFiles/pFst.dir/src/pFst.cpp.o.d -o CMakeFiles/pFst.dir/src/pFst.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/pFst.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 29%] Linking CXX executable pFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/pFst.dir/link.txt --verbose=1 -[ 29%] Built target segmentIhs -make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/depend -[ 30%] Linking CXX executable vcfld +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfclassify.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake "--color=" +[ 23%] Building CXX object CMakeFiles/smoother.dir/src/smoother.cpp.o make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfhetcount.dir/DependInfo.cmake "--color=" -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfld.dir/link.txt --verbose=1 +make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/build +[ 24%] Building CXX object CMakeFiles/plotHaps.dir/src/plotHaps.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/smoother.dir/src/smoother.cpp.o -MF CMakeFiles/smoother.dir/src/smoother.cpp.o.d -o CMakeFiles/smoother.dir/src/smoother.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/smoother.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 -fcf-protection -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 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu' -[ 30%] Linking CXX executable popStats -/usr/bin/cmake -E cmake_link_script CMakeFiles/popStats.dir/link.txt --verbose=1 -[ 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 -fcf-protection -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 pVst -/usr/bin/cmake -E cmake_link_script CMakeFiles/pVst.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 30%] Built target normalize-iHS -make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/depend +make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfhethomratio.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 -fcf-protection -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/vcfecho.dir/link.d CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -o vcfecho -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 30%] Linking CXX executable iHS -/usr/bin/cmake -E cmake_link_script CMakeFiles/iHS.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +make -f CMakeFiles/vcfnullgenofields.dir/build.make CMakeFiles/vcfnullgenofields.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/build +make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/build +[ 24%] Building CXX object CMakeFiles/vcfld.dir/src/vcfld.cpp.o make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/build +make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 30%] Built target vcfecho -make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcffilter.dir/DependInfo.cmake "--color=" -[ 30%] Linking CXX executable hapLrt -[ 30%] Building CXX object CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -/usr/bin/cmake -E cmake_link_script CMakeFiles/hapLrt.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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 -fcf-protection -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 -make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 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 -fcf-protection -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 -[ 31%] Linking CXX executable plotHaps -/usr/bin/cmake -E cmake_link_script CMakeFiles/plotHaps.dir/link.txt --verbose=1 -[ 31%] Linking CXX executable sequenceDiversity -/usr/bin/cmake -E cmake_link_script CMakeFiles/sequenceDiversity.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 31%] Built target smoother -[ 31%] Linking CXX executable bFst -make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/depend -/usr/bin/cmake -E cmake_link_script CMakeFiles/bFst.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcf2tsv.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/build +/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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfld.dir/src/vcfld.cpp.o -MF CMakeFiles/vcfld.dir/src/vcfld.cpp.o.d -o CMakeFiles/vcfld.dir/src/vcfld.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfld.cpp +make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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 -fcf-protection -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 -/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 -fcf-protection -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/permuteSmooth.dir/link.d CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -o permuteSmooth -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 32%] Built target permuteSmooth -make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfgenotypes.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu' -[ 32%] 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 -fcf-protection -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 -MF CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o.d -o CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfgenotypes.cpp -[ 32%] Linking CXX executable genotypeSummary -/usr/bin/cmake -E cmake_link_script CMakeFiles/genotypeSummary.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 -fcf-protection -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/abba-baba.dir/link.d "CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o" -o abba-baba -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 32%] Built target abba-baba -make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfannotategenotypes.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/build +make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/build +cd 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target wcFst -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/depend +[ 25%] Building CXX object CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o +make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/depend +make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/depend +make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/depend +[ 26%] Building CXX object CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o +make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg 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36%] Linking CXX executable vcfhetcount -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhetcount.dir/link.txt --verbose=1 -[ 36%] Linking CXX executable vcffilter -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffilter.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 36%] Built target vcfaltcount -make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfrandom.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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/vcfsamplenames.dir/src/vcfsamplenames.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -MF CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o.d -o CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfsamplenames.cpp -[ 38%] Linking CXX executable vcfgenotypes -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypes.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfflatten.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 38%] Built target pVst -make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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 -fcf-protection -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 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfprimers.dir/DependInfo.cmake "--color=" +[ 27%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -MF CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o.d -o CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/normalize-iHS.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 -fcf-protection -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 +[ 28%] Building CXX object CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o +make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/build make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/build +[ 28%] Building CXX object CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o +[ 28%] Building CXX object CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 39%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -MF CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o.d -o CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfgenotypecompare.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 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-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcffixup.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 28%] 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 -fcf-protection -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 +/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 -fcf-protection -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 make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/build +/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 -fcf-protection -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 +/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 -fcf-protection -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 make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 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 -fcf-protection -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 -/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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 -fcf-protection -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/iHS.dir/link.d CMakeFiles/iHS.dir/src/iHS.cpp.o -o iHS -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 40%] Built target plotHaps -make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfclassify.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 40%] Built target iHS -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfsamplediff.dir/DependInfo.cmake "--color=" -[ 40%] Built target genotypeSummary -make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/depend +[ 29%] Building CXX object CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o +make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/depend +/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 -fcf-protection -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]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake "--color=" -[ 41%] 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 -fcf-protection -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 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/build +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfnumalt.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 41%] 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 -fcf-protection -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 -[ 41%] 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 -fcf-protection -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 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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 -fcf-protection -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 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CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfannotategenotypes.cpp +[ 32%] 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 -fcf-protection -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 +/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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include 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-Wl,--dependency-file=CMakeFiles/bFst.dir/link.d CMakeFiles/bFst.dir/src/bFst.cpp.o -o bFst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/build make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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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CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfprimers.dir/DependInfo.cmake "--color=" +make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/build make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu' +[ 32%] Building CXX object CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/build +[ 32%] Building CXX object CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o +[ 33%] Building CXX object CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o +make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/build +/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 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CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o +make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/build +/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 -fcf-protection -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 -MF CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o.d -o CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfgenotypes.cpp make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 42%] 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 -fcf-protection -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 -/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so 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/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfnumalt.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 -fcf-protection -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 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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 -fcf-protection -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 -[ 43%] Linking CXX executable vcfcommonsamples -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcommonsamples.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so 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libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 44%] Built target vcfnullgenofields +[ 39%] Built target segmentIhs make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfannotate.dir/DependInfo.cmake "--color=" -/usr/bin/c++ -g 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normalize-iHS +/usr/bin/cmake -E cmake_link_script CMakeFiles/normalize-iHS.dir/link.txt --verbose=1 +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfclassify.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepsamples.dir/link.txt --verbose=1 make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 45%] Built target vcfgenotypes +[ 40%] 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 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/usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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 -fcf-protection -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/dumpContigsFromHeader.dir/link.d CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -o dumpContigsFromHeader -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so 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/usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 43%] Built target permuteSmooth make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 48%] Built target vcfsamplenames make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu 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/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfkeepgeno.dir/DependInfo.cmake "--color=" +[ 43%] Built target vcfsamplenames +make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfafpath.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 49%] Building CXX object CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -MF CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o.d -o CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfkeepinfo.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 50%] Linking CXX executable vcfsamplediff -[ 50%] Built target vcfremovesamples -make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/depend +make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfkeepgeno.dir/DependInfo.cmake "--color=" -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplediff.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/build +make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 50%] Building CXX object CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o +[ 44%] Linking CXX executable vcfsamplediff +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplediff.dir/link.txt --verbose=1 +[ 43%] Linking CXX executable vcfflatten +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfflatten.dir/link.txt --verbose=1 +[ 44%] Building CXX object CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.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 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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 -fcf-protection -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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/usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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 -fcf-protection -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 +[ 45%] Linking CXX executable abba-baba +/usr/bin/cmake -E cmake_link_script CMakeFiles/abba-baba.dir/link.txt --verbose=1 +[ 45%] Linking CXX executable plotHaps +/usr/bin/cmake -E cmake_link_script CMakeFiles/plotHaps.dir/link.txt --verbose=1 +[ 45%] Linking CXX executable pVst +/usr/bin/cmake -E cmake_link_script CMakeFiles/pVst.dir/link.txt --verbose=1 +[ 46%] Linking CXX executable vcfnullgenofields +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfnullgenofields.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 50%] Built target vcffilter -make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/depend -[ 51%] Linking CXX executable vcfrandom -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandom.dir/link.txt --verbose=1 -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfafpath.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 51%] Built target vcfkeepsamples +[ 46%] Built target vcfkeepsamples make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcountalleles.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 51%] Built target vcfcommonsamples -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu' -make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/build +[ 47%] 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 -fcf-protection -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 +[ 48%] Linking CXX executable vcfremovesamples +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremovesamples.dir/link.txt --verbose=1 +[ 49%] Linking CXX executable vcfnumalt +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfnumalt.dir/link.txt --verbose=1 +[ 49%] Linking CXX executable vcffixup +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffixup.dir/link.txt --verbose=1 +[ 49%] Linking CXX executable vcfgenotypecompare +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypecompare.dir/link.txt --verbose=1 +[ 49%] Linking CXX executable vcfcommonsamples +[ 49%] Linking CXX executable vcfannotategenotypes +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotategenotypes.dir/link.txt --verbose=1 +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcommonsamples.dir/link.txt --verbose=1 +[ 50%] Linking CXX executable vcfprimers +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfprimers.dir/link.txt --verbose=1 +[ 51%] Linking CXX executable vcfgenotypes +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypes.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 51%] Built target normalize-iHS +[ 52%] Linking CXX executable vcfrandom +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandom.dir/link.txt --verbose=1 make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcflength.dir/DependInfo.cmake "--color=" -[ 51%] Built target meltEHH -make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/depend -[ 52%] 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 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'/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfdistance.dir/DependInfo.cmake "--color=" -[ 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 -fcf-protection -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 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu' -[ 53%] Building CXX object CMakeFiles/vcflength.dir/src/vcflength.cpp.o +[ 52%] 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 -fcf-protection -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 +/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 52%] Linking CXX executable vcf2tsv +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2tsv.dir/link.txt --verbose=1 +[ 52%] Built target smoother +make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfdistance.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 54%] Building CXX object CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o +[ 53%] 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 -fcf-protection -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 -/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 54%] Linking CXX executable wcFst +/usr/bin/cmake -E cmake_link_script CMakeFiles/wcFst.dir/link.txt --verbose=1 +[ 54%] Linking CXX executable meltEHH +/usr/bin/cmake -E cmake_link_script CMakeFiles/meltEHH.dir/link.txt --verbose=1 +[ 54%] Linking CXX executable hapLrt +/usr/bin/cmake -E cmake_link_script CMakeFiles/hapLrt.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 54%] Built target vcfclassify +[ 54%] Linking CXX executable genotypeSummary +/usr/bin/cmake -E cmake_link_script CMakeFiles/genotypeSummary.dir/link.txt --verbose=1 +[ 54%] Built target vcfhetcount make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/depend +[ 54%] Linking CXX executable popStats make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg 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-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -MF CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o.d -o CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfrandomsample.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 -fcf-protection -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/vcfprimers.dir/link.d CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -o vcfprimers -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-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 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CMakeFiles/vcfflatten.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfentropy.dir/DependInfo.cmake "--color=" +[ 54%] Linking CXX executable bFst +/usr/bin/cmake -E cmake_link_script CMakeFiles/bFst.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 55%] Linking CXX executable vcfld +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfld.dir/link.txt --verbose=1 [ 56%] Building CXX object 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp 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'/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/build +[ 56%] Linking CXX executable iHS make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +/usr/bin/cmake -E cmake_link_script CMakeFiles/iHS.dir/link.txt --verbose=1 [ 56%] 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 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -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 -[ 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 -/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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto 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/usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-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 -fcf-protection -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/vcfremoveaberrantgenotypes.dir/link.d CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -o vcfremoveaberrantgenotypes -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 58%] Linking CXX executable vcfkeepinfo -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepinfo.dir/link.txt --verbose=1 -[ 58%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 58%] Built target vcfsamplediff +[ 56%] Built target vcfprimers +[ 56%] Built target vcfremoveaberrantgenotypes make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcheck.dir/DependInfo.cmake "--color=" -[ 58%] Built target vcfrandom make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu 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make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/build -[ 59%] Linking CXX executable vcfannotate -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotate.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 60%] Building CXX object CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o +[ 57%] Building CXX object CMakeFiles/vcfcheck.dir/src/vcfcheck.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 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'/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 62%] Built target vcfannotategenotypes make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfremap.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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 -fcf-protection -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 -fcf-protection -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/vcfkeepinfo.dir/link.d CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -o vcfkeepinfo -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 62%] Built target vcfkeepinfo +[ 57%] Built target vcfhethomratio make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcf2fasta.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 -fcf-protection -Wdate-time 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'/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu' -[ 63%] Built target vcfoverlay -[ 63%] Built target vcfdistance +[ 57%] 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 -fcf-protection -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 +[ 57%] 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 -fcf-protection -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 +[ 58%] 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 -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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-Wl,--dependency-file=CMakeFiles/vcfgenotypes.dir/link.d CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -o vcfgenotypes -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 58%] Built target vcfgenotypes make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.12+dfsg 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-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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 58%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -MF CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o.d -o CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfsitesummarize.cpp +[ 58%] Linking CXX executable vcfcountalleles +[ 58%] Built target vcfnullgenofields +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcountalleles.dir/link.txt --verbose=1 make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/depend -/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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -MF CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o.d -o CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf2fasta.cpp make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfbreakmulti.dir/DependInfo.cmake "--color=" -[ 64%] Linking CXX executable vcfentropy -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfentropy.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-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 -fcf-protection -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/abba-baba.dir/link.d "CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o" -o abba-baba -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -MF CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o.d -o CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfsitesummarize.cpp -[ 65%] Building CXX object CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o +[ 58%] Linking CXX executable vcfaddinfo +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaddinfo.dir/link.txt --verbose=1 +[ 59%] Building CXX object CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -MF CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o.d -o CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfbreakmulti.cpp -[ 65%] Built target vcfkeepgeno -/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 -fcf-protection -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/vcfcountalleles.dir/link.d CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -o vcfcountalleles -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 59%] Built target abba-baba make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/depend -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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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-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 -fcf-protection -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 +[ 61%] Linking CXX executable vcfoverlay +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfoverlay.dir/link.txt --verbose=1 +[ 62%] Linking CXX executable vcfkeepgeno +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepgeno.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 62%] Built target vcfrandom +make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcat.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 -fcf-protection -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/vcfgenotypecompare.dir/link.d CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -o vcfgenotypecompare -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 65%] Built target vcfgenotypecompare +[ 62%] Built target vcfsamplediff make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/depend -[ 66%] Building CXX object CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfgenosummarize.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 -fcf-protection -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 +[ 63%] 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 -fcf-protection -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 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 67%] 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 -fcf-protection -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 -[ 68%] Linking CXX executable vcfglxgt -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglxgt.dir/link.txt --verbose=1 -[ 69%] Building CXX object CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o +[ 64%] Linking CXX executable vcfkeepinfo +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepinfo.dir/link.txt --verbose=1 +[ 65%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -MF CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o.d -o CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfgenosummarize.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 -fcf-protection -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/vcfflatten.dir/link.d CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -o vcfflatten -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 69%] Built target vcfflatten +[ 65%] Linking CXX executable vcfafpath +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfafpath.dir/link.txt --verbose=1 +[ 65%] Built target plotHaps make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfgenosamplenames.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 70%] 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 -fcf-protection -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 -[ 70%] Linking CXX executable vcfcheck -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcheck.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 70%] Built target vcflength +[ 65%] Linking CXX executable vcfannotate +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotate.dir/link.txt --verbose=1 +[ 66%] 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 -fcf-protection -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 +[ 66%] Built target vcffixup make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfgeno2haplo.dir/DependInfo.cmake "--color=" -[ 70%] Built target vcfafpath -make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/depend make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfleftalign.dir/DependInfo.cmake "--color=" make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 67%] 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 -fcf-protection -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 +/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 -fcf-protection -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/vcfcountalleles.dir/link.d CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -o vcfcountalleles -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 67%] Built target vcfcountalleles +make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfleftalign.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 71%] 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 -fcf-protection -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 -[ 71%] Building CXX object CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o +[ 67%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -MF CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o.d -o CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfleftalign.cpp -[ 72%] Linking CXX executable vcfuniq -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniq.dir/link.txt --verbose=1 -[ 73%] 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 -fcf-protection -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/vcfflatten.dir/link.d CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -o vcfflatten -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 67%] Built target vcfflatten make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcombine.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 74%] Building CXX object CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o +[ 68%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniqalleles.dir/link.txt --verbose=1 -[ 76%] Built target vcfcheck +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcheck.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now 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/usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 76%] 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 -fcf-protection -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 -[ 76%] Built target vcfentropy +[ 71%] Built target popStats make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcf2dag.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu' -[ 77%] Building CXX object CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o +[ 71%] 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 -fcf-protection -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 +[ 72%] 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 -fcf-protection -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 -[ 77%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -g -O2 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/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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfsample2info.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 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-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 -fcf-protection -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 +[ 73%] Built target pFst make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfqual2info.dir/DependInfo.cmake "--color=" -[ 78%] Linking CXX executable vcfevenregions -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfevenregions.dir/link.txt --verbose=1 +[ 74%] Linking CXX executable vcfuniqalleles +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniqalleles.dir/link.txt --verbose=1 +[ 74%] Built target vcffilter +make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/depend +[ 74%] Building CXX object CMakeFiles/vcfsample2info.dir/src/vcfsample2info.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 -fcf-protection -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 +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfinfo2qual.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 78%] 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 -fcf-protection -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 -fcf-protection -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/vcfannotate.dir/link.d CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -o vcfannotate -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 78%] Built target vcfannotate -make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd 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CMakeFiles/vcfgenosamplenames.dir/link.txt --verbose=1 -[ 78%] 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 -fcf-protection -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 -[ 78%] Linking CXX executable vcfcat -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcat.dir/link.txt --verbose=1 -[ 79%] Linking CXX executable vcfremap -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremap.dir/link.txt --verbose=1 -[ 79%] Linking CXX executable vcfgenosummarize -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosummarize.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 74%] 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 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/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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfglbound.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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 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/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfinfosummarize.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 81%] Linking CXX executable vcfgeno2alleles -[ 81%] Building CXX object CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -[ 81%] Linking CXX executable vcfindex -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2alleles.dir/link.txt --verbose=1 +[ 74%] 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 -fcf-protection -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 +[ 74%] Building CXX object CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o +[ 74%] Linking CXX executable vcf2fasta +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2fasta.dir/link.txt --verbose=1 /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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -MF CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o.d -o CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfinfosummarize.cpp -/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 81%] Built target vcfgenosamplenames +[ 74%] Built target vcfkeepgeno make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake "--color=" -[ 81%] Built target vcfsitesummarize -make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfallelicprimitives.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/build -[ 82%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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 -fcf-protection -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 -[ 83%] Building CXX object CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -/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 -fcf-protection -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 +/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 83%] Built target vcfcat +[ 74%] Built target genotypeSummary +make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfallelicprimitives.dir/DependInfo.cmake "--color=" +[ 75%] 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 -fcf-protection -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 +[ 75%] Built target vcfafpath make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcleancomplex.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-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 -fcf-protection -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/iHS.dir/link.d CMakeFiles/iHS.dir/src/iHS.cpp.o -o iHS -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 84%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o +[ 76%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o +[ 76%] Built target iHS +/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 -fcf-protection -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 +[ 77%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.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 -fcf-protection -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/vcfcleancomplex.cpp.o -MF CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o.d -o CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfcleancomplex.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 77%] 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/legacy.cpp.o -MF CMakeFiles/vcfallelicprimitives.dir/src/legacy.cpp.o.d -o CMakeFiles/vcfallelicprimitives.dir/src/legacy.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/legacy.cpp +[ 78%] Linking CXX executable vcfintersect +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfintersect.dir/link.txt --verbose=1 +[ 79%] Linking CXX executable vcfglxgt +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglxgt.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 -fcf-protection -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/vcfkeepinfo.dir/link.d CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -o vcfkeepinfo -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 79%] Built target vcfkeepinfo +[ 80%] 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 -fcf-protection -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 +[ 80%] Linking CXX executable vcfevenregions +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfevenregions.dir/link.txt --verbose=1 +[ 80%] Linking CXX executable vcfbreakmulti +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfbreakmulti.dir/link.txt --verbose=1 +[ 80%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 84%] Built target vcfstreamsort +/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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro 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/build/reproducible-path/libvcflib-1.0.12+dfsg /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfparsealts.dir/DependInfo.cmake "--color=" +[ 81%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 84%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o +[ 81%] Built target vcfoverlay +[ 81%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcfparsealts.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 -fcf-protection -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/vcfparsealts.cpp.o -MF CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o.d -o CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfparsealts.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 82%] 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 -fcf-protection -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 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.12+dfsg=. -fstack-protector-strong 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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 -fcf-protection -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/vcfdistance.dir/link.d CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -o vcfdistance -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 83%] Built target vcfdistance +/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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 -fcf-protection -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/vcfgenotypecompare.dir/link.d CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -o vcfgenotypecompare -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 84%] Linking CXX executable vcfsitesummarize +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsitesummarize.dir/link.txt --verbose=1 +[ 84%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcf-wfa.cpp.o +[ 84%] Built target vcfgenotypecompare +/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 -fcf-protection -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 +[ 84%] Built target vcfuniq make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/depend -[ 84%] Linking CXX executable vcfcombine make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfroc.dir/DependInfo.cmake "--color=" -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcombine.dir/link.txt --verbose=1 -[ 85%] Linking CXX executable vcfsample2info +[ 85%] 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 -fcf-protection -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 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/build -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsample2info.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' [ 85%] 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 -fcf-protection -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/vcfroc.cpp.o -MF CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o.d -o CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcfroc.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 -fcf-protection -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/vcfintersect.dir/link.d CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -o vcfintersect -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 86%] Linking CXX executable vcfqual2info -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfqual2info.dir/link.txt --verbose=1 -[ 86%] Built target vcfintersect -[ 87%] 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 -fcf-protection -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 -/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 85%] Linking CXX executable vcfgenosamplenames +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosamplenames.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so 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--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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 85%] Built target vcfrandomsample +[ 86%] 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 -fcf-protection -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 +/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 86%] Built target hapLrt +/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 89%] Built target vcfgenosummarize +[ 87%] 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 -fcf-protection -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 +[ 87%] Built target vcfld make -f CMakeFiles/vcfwave.dir/build.make CMakeFiles/vcfwave.dir/depend -[ 89%] Built target vcfgeno2alleles make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfwave.dir/DependInfo.cmake "--color=" -make -f CMakeFiles/pyvcflib.dir/build.make CMakeFiles/pyvcflib.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/pyvcflib.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu' +[ 87%] Built target vcfentropy +[ 87%] 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 -fcf-protection -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 +[ 88%] 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 -fcf-protection -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 +[ 89%] 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 -fcf-protection -Wdate-time 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-D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfindex.dir/link.d CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -o vcfindex -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 89%] Built target sequenceDiversity +[ 89%] 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 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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 -fcf-protection -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 +[ 90%] Linking CXX executable vcfinfo2qual +[ 90%] 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 -fcf-protection -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/cmake -E cmake_link_script CMakeFiles/vcfinfo2qual.dir/link.txt --verbose=1 +[ 91%] Linking CXX executable vcfindex +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfindex.dir/link.txt --verbose=1 +[ 92%] Linking CXX executable vcfsample2info +/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsample2info.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 92%] Built target vcfevenregions +make -f CMakeFiles/pyvcflib.dir/build.make CMakeFiles/pyvcflib.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 89%] Building CXX object CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o +cd /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/CMakeFiles/pyvcflib.dir/DependInfo.cmake "--color=" +[ 93%] Linking CXX executable vcfglbound +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglbound.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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 -fcf-protection -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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 90%] Building CXX object CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o +make -f CMakeFiles/pyvcflib.dir/build.make CMakeFiles/pyvcflib.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 94%] 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 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-fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/vcfqual2info.dir/link.d CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -o vcfqual2info -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 91%] Built target vcfqual2info -[ 91%] 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 -fcf-protection -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%] Built target vcfcat +[ 94%] Built target vcfglxgt +[ 95%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp 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/usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 96%] Built target vcfindex +/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 92%] Built target 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CMakeFiles/vcfallelicprimitives.dir/src/legacy.cpp.o.d -o CMakeFiles/vcfallelicprimitives.dir/src/legacy.cpp.o -c /build/reproducible-path/libvcflib-1.0.12+dfsg/src/legacy.cpp -[ 93%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include 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-fcf-protection -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 -[ 93%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 96%] Built target vcf2fasta +/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 94%] Linking CXX executable vcfinfosummarize -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfinfosummarize.dir/link.txt --verbose=1 -[ 94%] Built target vcf2dag -[ 95%] 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 -fcf-protection -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 /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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 95%] Built target vcfglbound -[ 95%] 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 -fcf-protection -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 /build/reproducible-path/libvcflib-1.0.12+dfsg/src/vcf-wfa.cpp -[ 96%] 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 -fcf-protection -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 +[ 96%] Built target vcfgeno2alleles +/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 -fcf-protection -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/vcfannotate.dir/link.d CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -o vcfannotate -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 96%] Built target vcfglbound +[ 96%] Built target vcfannotate +/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 96%] Built target vcfbreakmulti +/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 96%] Built target vcfgenosummarize +/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 -fcf-protection -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/vcfqual2info.dir/link.d CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -o vcfqual2info -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 96%] Built target vcfqual2info +/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 96%] Built target vcfstreamsort /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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' [ 96%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-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 -fcf-protection -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/vcfsample2info.dir/link.d CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -o vcfsample2info -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 96%] Built target vcfcombine -/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 96%] Built target vcfsample2info +/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 96%] Built target vcfcreatemulti -[ 97%] Linking CXX executable vcfroc -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfroc.dir/link.txt --verbose=1 +[ 96%] Built target vcfremap +/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 96%] Built target 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 96%] Built target vcf2dag +[ 97%] Linking CXX executable vcfwave +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfwave.dir/link.txt --verbose=1 +[ 98%] Linking CXX executable vcfcleancomplex [ 98%] Linking CXX executable vcfparsealts +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcleancomplex.dir/link.txt --verbose=1 /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfparsealts.dir/link.txt --verbose=1 -[ 99%] Linking CXX executable 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 98%] Linking CXX executable vcfallelicprimitives +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfallelicprimitives.dir/link.txt --verbose=1 +[ 98%] Built target vcfcreatemulti +[ 99%] Linking CXX executable vcfroc +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfroc.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 -fcf-protection -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/vcfintersect.dir/link.d CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -o vcfintersect -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[ 99%] Built target vcfintersect +/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[100%] Linking CXX executable vcfstats /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstats.dir/link.txt --verbose=1 +[100%] Built target vcfcombine /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 -fcf-protection -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/vcfgeno2haplo.dir/link.d CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o -o vcfgeno2haplo -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[ 99%] Built target vcfgeno2haplo -[ 99%] Linking CXX executable vcfcleancomplex -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcleancomplex.dir/link.txt --verbose=1 -[100%] Linking CXX executable vcfwave -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfwave.dir/link.txt --verbose=1 -[100%] Linking CXX executable vcfallelicprimitives -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfallelicprimitives.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[100%] Built target vcfgeno2haplo +/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[100%] Built target vcfstats +[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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[100%] Built target vcfparsealts -/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[100%] Built target vcfparsealts +/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' -[100%] Built target vcfcleancomplex -[100%] Linking CXX shared module pyvcflib.cpython-313-x86_64-linux-gnu.so -/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' +[100%] Built target vcfroc +[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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' [100%] Built target vcfallelicprimitives +[100%] Linking CXX shared module pyvcflib.cpython-313-x86_64-linux-gnu.so +/usr/bin/cmake -E cmake_link_script CMakeFiles/pyvcflib.dir/link.txt --verbose=1 /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 -fcf-protection -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-x86_64-linux-gnu.so CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o -Wl,-rpath,"\$ORIGIN:" libvcflib.so.2 -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 /usr/bin/strip /build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu/pyvcflib.cpython-313-x86_64-linux-gnu.so make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' @@ -2255,34 +2291,34 @@ cd test && ctest . Test project /build/reproducible-path/libvcflib-1.0.12+dfsg/test Start 1: realign -1/9 Test #1: realign .......................... Passed 0.12 sec +1/9 Test #1: realign .......................... Passed 0.07 sec Start 2: pyvcflib -2/9 Test #2: pyvcflib ......................... Passed 0.12 sec +2/9 Test #2: pyvcflib ......................... Passed 0.07 sec Start 3: vcflib-api -3/9 Test #3: vcflib-api ....................... Passed 0.12 sec +3/9 Test #3: vcflib-api ....................... Passed 0.07 sec Start 4: vcf2tsv -4/9 Test #4: vcf2tsv .......................... Passed 0.16 sec +4/9 Test #4: vcf2tsv .......................... Passed 0.10 sec Start 5: vcfallelicprimitives -5/9 Test #5: vcfallelicprimitives ............. Passed 1.52 sec +5/9 Test #5: vcfallelicprimitives ............. Passed 0.79 sec Start 6: vcfwave -6/9 Test #6: vcfwave .......................... Passed 0.62 sec +6/9 Test #6: vcfwave .......................... Passed 0.39 sec Start 7: vcffilter -7/9 Test #7: vcffilter ........................ Passed 0.23 sec +7/9 Test #7: vcffilter ........................ Passed 0.17 sec Start 8: vcfnulldotslashdot -8/9 Test #8: vcfnulldotslashdot ............... Passed 0.14 sec +8/9 Test #8: vcfnulldotslashdot ............... Passed 0.09 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) = 3.16 sec +Total Test time (real) = 1.81 sec cd .. && rm -f build make[1]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake - cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/libvcflib-1.0.12\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/libvcflib-1.0.12\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/libvcflib-1.0.12+dfsg -B/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -2516,95 +2552,95 @@ -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/include/vcflib/vcf-c-api.h -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/include/vcflib/vcf-wfa.h -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfkeepgeno.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/sequenceDiversity.1 -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcountalleles.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfremap.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfentropy.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfnullgenofields.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/plotHaps.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfhetcount.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfrandomsample.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfstreamsort.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfuniq.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcommonsamples.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfroc.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcleancomplex.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfuniqalleles.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/hapLrt.1 -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/permuteSmooth.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcf2fasta.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/hapLrt.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfhethomratio.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/permuteGPAT++.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/pVst.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfinfosummarize.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfkeepinfo.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfnulldotslashdot.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcommonsamples.1 -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfparsealts.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfremoveaberrantgenotypes.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfsitesummarize.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfannotate.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfafpath.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfallelicprimitives.1 -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcat.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/segmentIhs.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcflength.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/dumpContigsFromHeader.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfflatten.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfkeepinfo.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfuniq.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfrandomsample.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcombine.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/segmentFst.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfstats.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfentropy.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfrandom.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/wcFst.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfleftalign.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfhetcount.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/meltEHH.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgenosummarize.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/plotHaps.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/iHS.1 -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfindex.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/permuteGPAT++.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfbreakmulti.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfinfo2qual.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcleancomplex.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgeno2haplo.1 -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfevenregions.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfld.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfsamplenames.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfoverlay.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfwave.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfstreamsort.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcflib-api.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcflength.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgenosamplenames.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfintersect.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/segmentIhs.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfannotate.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfsample2info.1 -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfprimers.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfglbound.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfaddinfo.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgenotypecompare.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfallelicprimitives.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfkeepgeno.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/wcFst.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/smoother.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/pVst.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfsamplediff.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfinfo2qual.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/pyvcflib.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfafpath.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/bFst.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfld.1 -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/genotypeSummary.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfdistance.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcheck.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfoverlay.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfremovesamples.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfecho.1 -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/popStats.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfhethomratio.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcf2fasta.1 -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcffixup.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcflib.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfleftalign.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcf2tsv.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfnulldotslashdot.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfecho.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfremovesamples.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfannotategenotypes.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfstats.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfrandom.1 -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/normalize-iHS.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/iHS.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcombine.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/meltEHH.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/sequenceDiversity.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcflib-api.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfbreakmulti.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfnullgenofields.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcf2dag.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgenotypecompare.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcf2tsv.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfroc.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfsitesummarize.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/pyvcflib.1 -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcffilter.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfaltcount.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfinfosummarize.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfintersect.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfannotategenotypes.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfkeepsamples.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfnumalt.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfsamplenames.1 -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcreatemulti.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfglbound.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcflib.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfremoveaberrantgenotypes.1 -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfglxgt.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcf2dag.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfremap.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfaltcount.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/dumpContigsFromHeader.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/abba-baba.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfsamplediff.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfflatten.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfdistance.1 -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfqual2info.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/segmentFst.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfuniqalleles.1 -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgeno2alleles.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfnumalt.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfclassify.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/smoother.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfaddinfo.1 -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/pFst.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgenosummarize.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfkeepsamples.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/bFst.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfsample2info.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/abba-baba.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgeno2haplo.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfwave.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfclassify.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfcheck.1 -- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgenotypes.1 --- Installing: /build/reproducible-path/libvcflib-1.0.12+dfsg/debian/tmp/usr/man/man1/vcfgenosamplenames.1 make[1]: Leaving directory '/build/reproducible-path/libvcflib-1.0.12+dfsg/obj-x86_64-linux-gnu' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/libvcflib-1.0.12+dfsg' @@ -2657,9 +2693,9 @@ 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-dev' in '../libvcflib-dev_1.0.12+dfsg-1_amd64.deb'. -dpkg-deb: building package 'libvcflib2-dbgsym' in '../libvcflib2-dbgsym_1.0.12+dfsg-1_amd64.deb'. dpkg-deb: building package 'libvcflib2' in '../libvcflib2_1.0.12+dfsg-1_amd64.deb'. +dpkg-deb: building package 'libvcflib2-dbgsym' in '../libvcflib2-dbgsym_1.0.12+dfsg-1_amd64.deb'. +dpkg-deb: building package 'libvcflib-dev' in '../libvcflib-dev_1.0.12+dfsg-1_amd64.deb'. dpkg-deb: building package 'libvcflib-tools' in '../libvcflib-tools_1.0.12+dfsg-1_amd64.deb'. dpkg-deb: building package 'libvcflib-tools-dbgsym' in '../libvcflib-tools-dbgsym_1.0.12+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../libvcflib_1.0.12+dfsg-1_amd64.buildinfo @@ -2669,12 +2705,14 @@ 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/337771/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/337771/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/2924260 and its subdirectories -I: Current time: Sun Feb 16 12:18:19 -12 2025 -I: pbuilder-time-stamp: 1739751500 +I: removing directory /srv/workspace/pbuilder/337771 and its subdirectories +I: Current time: Sun Mar 22 20:45:04 +14 2026 +I: pbuilder-time-stamp: 1774161904